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Showing metabocard for Tridecanoyl-CoA (HMDB0013109)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (6) Show 6 proteinsXML
enzymes (6) Show 6 proteins
Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-07-25 00:19:59 UTC
Update Date2022-03-07 02:51:28 UTC
HMDB IDHMDB0013109
Secondary Accession Numbers
  • HMDB13109
Metabolite Identification
Common NameTridecanoyl-CoA
DescriptionTridecanoyl-CoA is an acyl-CoA with C-13 fatty acid group as the acyl moiety. Acyl-CoA (or formyl-CoA) is a coenzyme involved in the metabolism of fatty acids. It is a temporary compound formed when coenzyme A (CoA) attaches to the end of a long-chain fatty acid inside living cells. The compound undergoes beta oxidation, forming one or more molecules of acetyl-CoA. This, in turn, enters the citric acid cycle, eventually forming several molecules of ATP. Tridecanoyl-CoA is involved in Phytanic acid peroxisomal oxidation pathway as an intermediate reduction product.
Structure
Data?1582753089
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0013109 (Tridecanoyl-CoA)


  Mrv1652303262014182D          

 62 64  0  0  1  0            999 V2000
   18.5660  -10.0552    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.7375  -10.8621    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.1181   -9.4421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.7056   -8.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.4912  -11.1977    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.4050  -12.0182    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.8986   -8.8991    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.8123   -9.7197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1855  -11.4752    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5980  -12.1897    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   19.1181   -8.0132    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9431   -9.4421    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.0181  -12.5703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.9431   -8.0132    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.2624  -12.9435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.3556   -8.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4420  -13.0297    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.2057  -10.7852    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7056   -7.2987    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.8466  -13.3773    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
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   17.1064  -13.7834    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   16.7709  -14.5370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   10.3931  -13.0522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   12.8546  -12.7934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    7.2974  -11.2222    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
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  2  1  1  1  0  0  0
  3  1  1  0  0  0  0
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 11  4  1  0  0  0  0
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 10  6  1  0  0  0  0
  8  7  2  0  0  0  0
 10  9  1  0  0  0  0
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 62 61  1  0  0  0  0
M  END
Download

3D MOL for HMDB0013109 (Tridecanoyl-CoA)

HMDB0013109
     RDKit          3D
Tridecanoyl-CoA
122124  0  0  0  0  0  0  0  0999 V2000
   -3.4526   -3.5772    5.7728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3301   -4.4903    5.3191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6206   -3.8254    4.1560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5347   -3.6215    2.9803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7808   -2.9597    1.8630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2542   -1.5903    2.2145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5537   -1.0605    0.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1110    0.3686    1.1990 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5747    0.9251   -0.0388 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8321    2.4091    0.1440 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5028    2.9693   -1.0653 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9516    2.5841   -1.2173 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5897    3.1746    0.0225 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0162    2.3132    0.8061 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7121    4.8583    0.3143 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.2568    6.1114   -0.8191 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4265    7.2244   -0.1557 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1376    6.7524    0.3085 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1476    6.2931   -0.5933 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3495    6.3446   -1.8173 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1279    5.7240   -0.0825 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6667    4.7654   -1.1264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8009    3.9848   -0.6769 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2914    2.9264   -1.5274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6691    2.7957   -2.6328 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.3139    0.5980   -1.5310 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.3512    0.4459   -2.9648 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8186   -0.5229   -2.1233 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.0374   -2.1443   -3.2189 P   0  0  0  0  0  5  0  0  0  0  0  0
    0.8367   -1.4971   -4.3070 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6915   -3.5475   -3.8624 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.1832   -2.8909   -2.4264 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2583   -3.2605   -1.4744 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.5747   -2.2458   -0.5713 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9468   -2.8874    0.6167 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.0002   -1.9431    1.6889 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.7647   -0.8371    1.6378 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.6250   -0.1467    2.7588 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7585   -0.7903    3.5721 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2588   -0.5302    4.8181 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6556    0.6246    5.5186 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.3730   -1.4324    5.3343 N   0  0  0  0  0  0  0  0  0  0  0  0
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    2.5223   -2.7739    3.4036 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3880   -1.9002    2.8859 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9023   -3.9381    0.7281 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.1527   -4.8935    1.6997 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0092   -4.5272   -0.6892 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.1908   -5.2745   -0.7839 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.0198   -6.8266   -1.3319 P   0  0  0  0  0  5  0  0  0  0  0  0
    4.5758   -6.8966   -2.7618 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9986   -7.9370   -0.4667 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4251   -7.3375   -1.4130 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9956   -2.5520    5.9122 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2441   -3.5977    5.0144 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8153   -3.8598    6.7850 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5879   -4.6095    6.1313 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7227   -5.4618    4.9278 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7194   -4.3585    3.8311 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2860   -2.8073    4.4837 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8722   -4.6269    2.5906 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4338   -3.0131    3.2186 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4620   -2.7987    0.9653 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9142   -3.5545    1.5074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5068   -1.6401    3.0438 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0814   -0.9494    2.5375 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2642   -1.1360    0.1005 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3413   -1.6942    0.8117 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6740    0.2943    1.9902 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9085    1.0022    1.5835 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5296    0.4346   -0.2454 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1835    0.8346   -0.8574 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5507    2.4850    1.0194 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1320    2.8903    0.4019 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9335    2.5352   -1.9565 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4028    4.0432   -1.1745 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3337    3.0858   -2.1195 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.1248    1.5054   -1.3081 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2218    6.6368   -1.1644 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6957    5.8436   -1.7241 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3748    8.0599   -0.8682 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0410    7.5819    0.7225 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9664    6.7657    1.3502 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8493    6.5334    0.1294 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9493    5.1507    0.8406 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1243    5.4685   -1.9158 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9145    4.1928   -1.6522 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2183    4.2243    0.2391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8845    1.2314   -0.4890 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0458    2.3994    0.7633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7949    0.0172   -2.3578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8521   -0.1672   -0.8732 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0581    1.2223   -1.0075 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.6689    2.9286   -2.4824 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1395    3.2772   -3.3056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1803    2.0385   -4.0182 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6270    1.0043   -3.5493 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0697   -0.0659   -3.6541 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8065   -3.4083   -2.0747 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1234   -3.9749   -4.5702 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4775   -2.0505   -3.0980 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9940   -3.7458   -3.1085 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1961   -3.3727   -2.1165 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9374   -3.3644    0.4044 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4234   -0.5161    0.8203 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3522    0.5851    6.2962 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2588    1.5560    5.2795 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3065   -3.1870    5.1228 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8810   -3.5171    0.7865 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4721   -5.5999    1.5887 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1067   -5.0587   -0.9771 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8391   -7.7481    0.4881 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2797   -8.0142   -0.7073 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
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 55118  1  1
 56119  1  0
 57120  1  6
 61121  1  0
 62122  1  0
M  END
Download

3D SDF for HMDB0013109 (Tridecanoyl-CoA)


  Mrv1652303262014182D          

 62 64  0  0  1  0            999 V2000
   18.5660  -10.0552    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.7375  -10.8621    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.1181   -9.4421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.7056   -8.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.4912  -11.1977    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   19.4050  -12.0182    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.8986   -8.8991    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   17.8123   -9.7197    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.1855  -11.4752    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5980  -12.1897    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   19.1181   -8.0132    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9431   -9.4421    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   20.0181  -12.5703    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.9431   -8.0132    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.2624  -12.9435    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.3556   -8.7276    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.4420  -13.0297    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.2057  -10.7852    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7056   -7.2987    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.8466  -13.3773    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   19.0396  -13.2057    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.6535  -13.5488    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.6750  -14.1842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1064  -13.7834    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   16.7709  -14.5370    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8601  -14.1190    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3528  -13.4478    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.9504  -14.6233    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   15.1299  -14.7095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.0366  -15.4437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.8642  -13.8028    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7823  -11.8897    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.6028  -11.8034    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0877  -12.4709    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    9.9082  -12.3847    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3931  -13.0522    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2137  -12.9659    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6985  -13.6333    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.5190  -13.5471    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.0040  -14.2145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8244  -14.1283    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6449  -14.0421    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7382  -13.3078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9107  -14.9488    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6684  -14.9682    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8546  -12.7934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.2438  -11.6310    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2974  -11.2222    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.4769  -11.3085    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9920  -10.6411    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1413  -12.0622    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3276   -9.8873    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8426   -9.2199    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1782   -8.4662    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6933   -7.7988    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0289   -7.0451    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5439   -6.3776    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8795   -5.6239    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3946   -4.9565    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7302   -4.2028    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2453   -3.5354    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.5809   -2.7817    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  3  1  1  0  0  0  0
  8  1  1  0  0  0  0
  5  2  1  0  0  0  0
  9  2  1  0  0  0  0
  4  3  2  0  0  0  0
 12  3  1  0  0  0  0
 11  4  1  0  0  0  0
  7  4  1  0  0  0  0
  6  5  1  0  0  0  0
  5 18  1  6  0  0  0
  6 13  1  6  0  0  0
 10  6  1  0  0  0  0
  8  7  2  0  0  0  0
 10  9  1  0  0  0  0
 10 15  1  1  0  0  0
 19 11  1  0  0  0  0
 14 11  2  0  0  0  0
 16 12  2  0  0  0  0
 20 13  1  0  0  0  0
 16 14  1  0  0  0  0
 17 15  1  0  0  0  0
 24 17  1  0  0  0  0
 21 20  1  0  0  0  0
 22 20  2  0  0  0  0
 23 20  1  0  0  0  0
 25 24  1  0  0  0  0
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 28 25  1  0  0  0  0
 29 28  1  0  0  0  0
 30 28  2  0  0  0  0
 31 28  1  0  0  0  0
 42 29  1  0  0  0  0
 33 32  1  0  0  0  0
 48 32  1  0  0  0  0
 34 33  1  0  0  0  0
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 47 35  2  0  0  0  0
 37 36  1  0  0  0  0
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 43 41  1  0  0  0  0
 44 41  1  0  0  0  0
 49 48  1  0  0  0  0
 50 49  1  0  0  0  0
 51 49  2  0  0  0  0
 52 50  1  0  0  0  0
 53 52  1  0  0  0  0
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 56 55  1  0  0  0  0
 57 56  1  0  0  0  0
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 59 58  1  0  0  0  0
 60 59  1  0  0  0  0
 61 60  1  0  0  0  0
 62 61  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0013109

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N

> <INCHI_IDENTIFIER>
InChI=1S/C34H60N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-25(43)62-18-17-36-24(42)15-16-37-32(46)29(45)34(2,3)20-55-61(52,53)58-60(50,51)54-19-23-28(57-59(47,48)49)27(44)33(56-23)41-22-40-26-30(35)38-21-39-31(26)41/h21-23,27-29,33,44-45H,4-20H2,1-3H3,(H,36,42)(H,37,46)(H,50,51)(H,52,53)(H2,35,38,39)(H2,47,48,49)/t23-,27-,28-,29?,33-/m1/s1

> <INCHI_KEY>
TZKUYUHMJHEXOQ-XILBVEEWSA-N

> <FORMULA>
C34H60N7O17P3S

> <MOLECULAR_WEIGHT>
963.863

> <EXACT_MASS>
963.297923755

> <JCHEM_ACCEPTOR_COUNT>
17

> <JCHEM_ATOM_COUNT>
122

> <JCHEM_AVERAGE_POLARIZABILITY>
93.93398852253654

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-({[hydroxy({[hydroxy({3-hydroxy-2,2-dimethyl-3-[(2-{[2-(tridecanoylsulfanyl)ethyl]carbamoyl}ethyl)carbamoyl]propoxy})phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-3-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
1.59

> <JCHEM_LOGP>
-0.7353966161479604

> <ALOGPS_LOGS>
-2.60

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.9001207347761846

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8209787813398228

> <JCHEM_PKA_STRONGEST_BASIC>
4.006053268556904

> <JCHEM_POLAR_SURFACE_AREA>
363.6299999999999

> <JCHEM_REFRACTIVITY>
222.84490000000002

> <JCHEM_ROTATABLE_BOND_COUNT>
31

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.43e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-({[hydroxy([hydroxy(3-hydroxy-2,2-dimethyl-3-[(2-{[2-(tridecanoylsulfanyl)ethyl]carbamoyl}ethyl)carbamoyl]propoxy)phosphoryl]oxy)phosphoryl]oxy}methyl)oxolan-3-yl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0013109 (Tridecanoyl-CoA)

HMDB0013109
     RDKit          3D
Tridecanoyl-CoA
122124  0  0  0  0  0  0  0  0999 V2000
   -3.4526   -3.5772    5.7728 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3301   -4.4903    5.3191 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6206   -3.8254    4.1560 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5347   -3.6215    2.9803 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7808   -2.9597    1.8630 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2542   -1.5903    2.2145 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5537   -1.0605    0.9510 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1110    0.3686    1.1990 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5747    0.9251   -0.0388 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8321    2.4091    0.1440 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5028    2.9693   -1.0653 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9516    2.5841   -1.2173 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5897    3.1746    0.0225 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0162    2.3132    0.8061 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7121    4.8583    0.3143 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.2568    6.1114   -0.8191 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4265    7.2244   -0.1557 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.1376    6.7524    0.3085 N   0  0  0  0  0  0  0  0  0  0  0  0
    0.1476    6.2931   -0.5933 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3495    6.3446   -1.8173 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1279    5.7240   -0.0825 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6667    4.7654   -1.1264 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8009    3.9848   -0.6769 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2914    2.9264   -1.5274 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6691    2.7957   -2.6328 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.1234   -3.9749   -4.5702 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0013109 (Tridecanoyl-CoA)

HEADER    PROTEIN                                 26-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   26-MAR-20         0                                  
HETATM    1  N   UNK     0      34.657 -18.770   0.000  0.00  0.00           N+0
HETATM    2  C   UNK     0      34.977 -20.276   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      35.687 -17.625   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      34.917 -16.292   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      36.384 -20.902   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      36.223 -22.434   0.000  0.00  0.00           C+0
HETATM    7  N   UNK     0      33.411 -16.612   0.000  0.00  0.00           N+0
HETATM    8  C   UNK     0      33.250 -18.143   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      33.946 -21.420   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0      34.716 -22.754   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      35.687 -14.958   0.000  0.00  0.00           C+0
HETATM   12  N   UNK     0      37.227 -17.625   0.000  0.00  0.00           N+0
HETATM   13  O   UNK     0      37.367 -23.465   0.000  0.00  0.00           O+0
HETATM   14  N   UNK     0      37.227 -14.958   0.000  0.00  0.00           N+0
HETATM   15  C   UNK     0      34.090 -24.161   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      37.997 -16.292   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      32.558 -24.322   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      37.717 -20.132   0.000  0.00  0.00           O+0
HETATM   19  N   UNK     0      34.917 -13.624   0.000  0.00  0.00           N+0
HETATM   20  P   UNK     0      37.047 -24.971   0.000  0.00  0.00           P+0
HETATM   21  O   UNK     0      35.541 -24.651   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      38.553 -25.291   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      36.727 -26.477   0.000  0.00  0.00           O+0
HETATM   24  P   UNK     0      31.932 -25.729   0.000  0.00  0.00           P+0
HETATM   25  O   UNK     0      31.306 -27.136   0.000  0.00  0.00           O+0
HETATM   26  O   UNK     0      33.339 -26.355   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      30.525 -25.103   0.000  0.00  0.00           O+0
HETATM   28  P   UNK     0      29.774 -27.297   0.000  0.00  0.00           P+0
HETATM   29  O   UNK     0      28.242 -27.458   0.000  0.00  0.00           O+0
HETATM   30  O   UNK     0      29.935 -28.828   0.000  0.00  0.00           O+0
HETATM   31  O   UNK     0      29.613 -25.765   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      14.527 -22.194   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      16.059 -22.033   0.000  0.00  0.00           C+0
HETATM   34  N   UNK     0      16.964 -23.279   0.000  0.00  0.00           N+0
HETATM   35  C   UNK     0      18.495 -23.118   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      19.400 -24.364   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      20.932 -24.203   0.000  0.00  0.00           C+0
HETATM   38  N   UNK     0      21.837 -25.449   0.000  0.00  0.00           N+0
HETATM   39  C   UNK     0      23.369 -25.288   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      24.274 -26.534   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      25.806 -26.373   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      27.337 -26.212   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      25.645 -24.841   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      25.967 -27.904   0.000  0.00  0.00           C+0
HETATM   45  O   UNK     0      23.648 -27.941   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0      23.995 -23.881   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0      19.122 -21.711   0.000  0.00  0.00           O+0
HETATM   48  S   UNK     0      13.622 -20.948   0.000  0.00  0.00           S+0
HETATM   49  C   UNK     0      12.090 -21.109   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      11.185 -19.863   0.000  0.00  0.00           C+0
HETATM   51  O   UNK     0      11.464 -22.516   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0      11.812 -18.456   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      10.906 -17.210   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      11.533 -15.804   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      10.627 -14.558   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      11.254 -13.151   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      10.349 -11.905   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      10.975 -10.498   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      10.070  -9.252   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      10.696  -7.845   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       9.791  -6.599   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0      10.418  -5.193   0.000  0.00  0.00           C+0
CONECT    1    2    3    8                                                  
CONECT    2    1    5    9                                                  
CONECT    3    1    4   12                                                  
CONECT    4    3   11    7                                                  
CONECT    5    2    6   18                                                  
CONECT    6    5   13   10                                                  
CONECT    7    4    8                                                       
CONECT    8    1    7                                                       
CONECT    9    2   10                                                       
CONECT   10    6    9   15                                                  
CONECT   11    4   19   14                                                  
CONECT   12    3   16                                                       
CONECT   13    6   20                                                       
CONECT   14   11   16                                                       
CONECT   15   10   17                                                       
CONECT   16   12   14                                                       
CONECT   17   15   24                                                       
CONECT   18    5                                                            
CONECT   19   11                                                            
CONECT   20   13   21   22   23                                             
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   20                                                            
CONECT   24   17   25   26   27                                             
CONECT   25   24   28                                                       
CONECT   26   24                                                            
CONECT   27   24                                                            
CONECT   28   25   29   30   31                                             
CONECT   29   28   42                                                       
CONECT   30   28                                                            
CONECT   31   28                                                            
CONECT   32   33   48                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36   47                                                  
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40   46                                                  
CONECT   40   39   41   45                                                  
CONECT   41   40   42   43   44                                             
CONECT   42   29   41                                                       
CONECT   43   41                                                            
CONECT   44   41                                                            
CONECT   45   40                                                            
CONECT   46   39                                                            
CONECT   47   35                                                            
CONECT   48   32   49                                                       
CONECT   49   48   50   51                                                  
CONECT   50   49   52                                                       
CONECT   51   49                                                            
CONECT   52   50   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61                                                            
MASTER        0    0    0    0    0    0    0    0   62    0  128    0
END
Download

3D PDB for HMDB0013109 (Tridecanoyl-CoA)

COMPND    HMDB0013109
HETATM    1  C1  UNL     1      -3.453  -3.577   5.773  1.00  0.00           C  
HETATM    2  C2  UNL     1      -2.330  -4.490   5.319  1.00  0.00           C  
HETATM    3  C3  UNL     1      -1.621  -3.825   4.156  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.535  -3.622   2.980  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.781  -2.960   1.863  1.00  0.00           C  
HETATM    6  C6  UNL     1      -1.254  -1.590   2.215  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.554  -1.061   0.951  1.00  0.00           C  
HETATM    8  C8  UNL     1      -0.111   0.369   1.199  1.00  0.00           C  
HETATM    9  C9  UNL     1       0.575   0.925  -0.039  1.00  0.00           C  
HETATM   10  C10 UNL     1       0.832   2.409   0.144  1.00  0.00           C  
HETATM   11  C11 UNL     1       1.503   2.969  -1.065  1.00  0.00           C  
HETATM   12  C12 UNL     1       2.952   2.584  -1.217  1.00  0.00           C  
HETATM   13  C13 UNL     1       3.590   3.175   0.023  1.00  0.00           C  
HETATM   14  O1  UNL     1       4.016   2.313   0.806  1.00  0.00           O  
HETATM   15  S1  UNL     1       3.712   4.858   0.314  1.00  0.00           S  
HETATM   16  C14 UNL     1       3.257   6.111  -0.819  1.00  0.00           C  
HETATM   17  C15 UNL     1       2.426   7.224  -0.156  1.00  0.00           C  
HETATM   18  N1  UNL     1       1.138   6.752   0.308  1.00  0.00           N  
HETATM   19  C16 UNL     1       0.148   6.293  -0.593  1.00  0.00           C  
HETATM   20  O2  UNL     1       0.349   6.345  -1.817  1.00  0.00           O  
HETATM   21  C17 UNL     1      -1.128   5.724  -0.083  1.00  0.00           C  
HETATM   22  C18 UNL     1      -1.667   4.765  -1.126  1.00  0.00           C  
HETATM   23  N2  UNL     1      -2.801   3.985  -0.677  1.00  0.00           N  
HETATM   24  C19 UNL     1      -3.291   2.926  -1.527  1.00  0.00           C  
HETATM   25  O3  UNL     1      -2.669   2.796  -2.633  1.00  0.00           O  
HETATM   26  C20 UNL     1      -4.398   2.099  -1.098  1.00  0.00           C  
HETATM   27  O4  UNL     1      -5.205   2.690  -0.158  1.00  0.00           O  
HETATM   28  C21 UNL     1      -5.204   1.427  -2.165  1.00  0.00           C  
HETATM   29  C22 UNL     1      -6.314   0.598  -1.531  1.00  0.00           C  
HETATM   30  C23 UNL     1      -5.830   2.451  -3.053  1.00  0.00           C  
HETATM   31  C24 UNL     1      -4.351   0.446  -2.965  1.00  0.00           C  
HETATM   32  O5  UNL     1      -3.819  -0.523  -2.123  1.00  0.00           O  
HETATM   33  P1  UNL     1      -2.787  -1.594  -2.914  1.00  0.00           P  
HETATM   34  O6  UNL     1      -3.236  -1.742  -4.344  1.00  0.00           O  
HETATM   35  O7  UNL     1      -2.877  -3.113  -2.192  1.00  0.00           O  
HETATM   36  O8  UNL     1      -1.197  -0.998  -2.821  1.00  0.00           O  
HETATM   37  P2  UNL     1      -0.037  -2.144  -3.219  1.00  0.00           P  
HETATM   38  O9  UNL     1       0.837  -1.497  -4.307  1.00  0.00           O  
HETATM   39  O10 UNL     1      -0.692  -3.548  -3.862  1.00  0.00           O  
HETATM   40  O11 UNL     1       0.967  -2.539  -1.878  1.00  0.00           O  
HETATM   41  C25 UNL     1       2.183  -2.891  -2.426  1.00  0.00           C  
HETATM   42  C26 UNL     1       3.258  -3.261  -1.474  1.00  0.00           C  
HETATM   43  O12 UNL     1       3.575  -2.246  -0.571  1.00  0.00           O  
HETATM   44  C27 UNL     1       3.947  -2.887   0.617  1.00  0.00           C  
HETATM   45  N3  UNL     1       4.000  -1.943   1.689  1.00  0.00           N  
HETATM   46  C28 UNL     1       4.765  -0.837   1.638  1.00  0.00           C  
HETATM   47  N4  UNL     1       4.625  -0.147   2.759  1.00  0.00           N  
HETATM   48  C29 UNL     1       3.759  -0.790   3.572  1.00  0.00           C  
HETATM   49  C30 UNL     1       3.259  -0.530   4.818  1.00  0.00           C  
HETATM   50  N5  UNL     1       3.656   0.625   5.519  1.00  0.00           N  
HETATM   51  N6  UNL     1       2.373  -1.432   5.334  1.00  0.00           N  
HETATM   52  C31 UNL     1       2.024  -2.526   4.627  1.00  0.00           C  
HETATM   53  N7  UNL     1       2.522  -2.774   3.404  1.00  0.00           N  
HETATM   54  C32 UNL     1       3.388  -1.900   2.886  1.00  0.00           C  
HETATM   55  C33 UNL     1       2.902  -3.938   0.728  1.00  0.00           C  
HETATM   56  O13 UNL     1       3.153  -4.894   1.700  1.00  0.00           O  
HETATM   57  C34 UNL     1       3.009  -4.527  -0.689  1.00  0.00           C  
HETATM   58  O14 UNL     1       4.191  -5.274  -0.784  1.00  0.00           O  
HETATM   59  P3  UNL     1       4.020  -6.827  -1.332  1.00  0.00           P  
HETATM   60  O15 UNL     1       4.576  -6.897  -2.762  1.00  0.00           O  
HETATM   61  O16 UNL     1       4.999  -7.937  -0.467  1.00  0.00           O  
HETATM   62  O17 UNL     1       2.425  -7.338  -1.413  1.00  0.00           O  
HETATM   63  H1  UNL     1      -2.996  -2.552   5.912  1.00  0.00           H  
HETATM   64  H2  UNL     1      -4.244  -3.598   5.014  1.00  0.00           H  
HETATM   65  H3  UNL     1      -3.815  -3.860   6.785  1.00  0.00           H  
HETATM   66  H4  UNL     1      -1.588  -4.609   6.131  1.00  0.00           H  
HETATM   67  H5  UNL     1      -2.723  -5.462   4.928  1.00  0.00           H  
HETATM   68  H6  UNL     1      -0.719  -4.359   3.831  1.00  0.00           H  
HETATM   69  H7  UNL     1      -1.286  -2.807   4.484  1.00  0.00           H  
HETATM   70  H8  UNL     1      -2.872  -4.627   2.591  1.00  0.00           H  
HETATM   71  H9  UNL     1      -3.434  -3.013   3.219  1.00  0.00           H  
HETATM   72  H10 UNL     1      -2.462  -2.799   0.965  1.00  0.00           H  
HETATM   73  H11 UNL     1      -0.914  -3.554   1.507  1.00  0.00           H  
HETATM   74  H12 UNL     1      -0.507  -1.640   3.044  1.00  0.00           H  
HETATM   75  H13 UNL     1      -2.081  -0.949   2.538  1.00  0.00           H  
HETATM   76  H14 UNL     1      -1.264  -1.136   0.101  1.00  0.00           H  
HETATM   77  H15 UNL     1       0.341  -1.694   0.812  1.00  0.00           H  
HETATM   78  H16 UNL     1       0.674   0.294   1.990  1.00  0.00           H  
HETATM   79  H17 UNL     1      -0.908   1.002   1.584  1.00  0.00           H  
HETATM   80  H18 UNL     1       1.530   0.435  -0.245  1.00  0.00           H  
HETATM   81  H19 UNL     1      -0.183   0.835  -0.857  1.00  0.00           H  
HETATM   82  H20 UNL     1       1.551   2.485   1.019  1.00  0.00           H  
HETATM   83  H21 UNL     1      -0.132   2.890   0.402  1.00  0.00           H  
HETATM   84  H22 UNL     1       0.934   2.535  -1.956  1.00  0.00           H  
HETATM   85  H23 UNL     1       1.403   4.043  -1.175  1.00  0.00           H  
HETATM   86  H24 UNL     1       3.334   3.086  -2.119  1.00  0.00           H  
HETATM   87  H25 UNL     1       3.125   1.505  -1.308  1.00  0.00           H  
HETATM   88  H26 UNL     1       4.222   6.637  -1.164  1.00  0.00           H  
HETATM   89  H27 UNL     1       2.696   5.844  -1.724  1.00  0.00           H  
HETATM   90  H28 UNL     1       2.375   8.060  -0.868  1.00  0.00           H  
HETATM   91  H29 UNL     1       3.041   7.582   0.722  1.00  0.00           H  
HETATM   92  H30 UNL     1       0.966   6.766   1.350  1.00  0.00           H  
HETATM   93  H31 UNL     1      -1.849   6.533   0.129  1.00  0.00           H  
HETATM   94  H32 UNL     1      -0.949   5.151   0.841  1.00  0.00           H  
HETATM   95  H33 UNL     1      -2.124   5.469  -1.916  1.00  0.00           H  
HETATM   96  H34 UNL     1      -0.914   4.193  -1.652  1.00  0.00           H  
HETATM   97  H35 UNL     1      -3.218   4.224   0.239  1.00  0.00           H  
HETATM   98  H36 UNL     1      -3.884   1.231  -0.489  1.00  0.00           H  
HETATM   99  H37 UNL     1      -5.046   2.399   0.763  1.00  0.00           H  
HETATM  100  H38 UNL     1      -6.795   0.017  -2.358  1.00  0.00           H  
HETATM  101  H39 UNL     1      -5.852  -0.167  -0.873  1.00  0.00           H  
HETATM  102  H40 UNL     1      -7.058   1.222  -1.008  1.00  0.00           H  
HETATM  103  H41 UNL     1      -6.669   2.929  -2.482  1.00  0.00           H  
HETATM  104  H42 UNL     1      -5.140   3.277  -3.306  1.00  0.00           H  
HETATM  105  H43 UNL     1      -6.180   2.038  -4.018  1.00  0.00           H  
HETATM  106  H44 UNL     1      -3.627   1.004  -3.549  1.00  0.00           H  
HETATM  107  H45 UNL     1      -5.070  -0.066  -3.654  1.00  0.00           H  
HETATM  108  H46 UNL     1      -3.806  -3.408  -2.075  1.00  0.00           H  
HETATM  109  H47 UNL     1      -0.123  -3.975  -4.570  1.00  0.00           H  
HETATM  110  H48 UNL     1       2.477  -2.050  -3.098  1.00  0.00           H  
HETATM  111  H49 UNL     1       1.994  -3.746  -3.108  1.00  0.00           H  
HETATM  112  H50 UNL     1       4.196  -3.373  -2.116  1.00  0.00           H  
HETATM  113  H51 UNL     1       4.937  -3.364   0.404  1.00  0.00           H  
HETATM  114  H52 UNL     1       5.423  -0.516   0.820  1.00  0.00           H  
HETATM  115  H53 UNL     1       4.352   0.585   6.296  1.00  0.00           H  
HETATM  116  H54 UNL     1       3.259   1.556   5.279  1.00  0.00           H  
HETATM  117  H55 UNL     1       1.306  -3.187   5.123  1.00  0.00           H  
HETATM  118  H56 UNL     1       1.881  -3.517   0.786  1.00  0.00           H  
HETATM  119  H57 UNL     1       2.472  -5.600   1.589  1.00  0.00           H  
HETATM  120  H58 UNL     1       2.107  -5.059  -0.977  1.00  0.00           H  
HETATM  121  H59 UNL     1       4.839  -7.748   0.488  1.00  0.00           H  
HETATM  122  H60 UNL     1       2.280  -8.014  -0.707  1.00  0.00           H  
CONECT    1    2   63   64   65
CONECT    2    3   66   67
CONECT    3    4   68   69
CONECT    4    5   70   71
CONECT    5    6   72   73
CONECT    6    7   74   75
CONECT    7    8   76   77
CONECT    8    9   78   79
CONECT    9   10   80   81
CONECT   10   11   82   83
CONECT   11   12   84   85
CONECT   12   13   86   87
CONECT   13   14   14   15
CONECT   15   16
CONECT   16   17   88   89
CONECT   17   18   90   91
CONECT   18   19   92
CONECT   19   20   20   21
CONECT   21   22   93   94
CONECT   22   23   95   96
CONECT   23   24   97
CONECT   24   25   25   26
CONECT   26   27   28   98
CONECT   27   99
CONECT   28   29   30   31
CONECT   29  100  101  102
CONECT   30  103  104  105
CONECT   31   32  106  107
CONECT   32   33
CONECT   33   34   34   35   36
CONECT   35  108
CONECT   36   37
CONECT   37   38   38   39   40
CONECT   39  109
CONECT   40   41
CONECT   41   42  110  111
CONECT   42   43   57  112
CONECT   43   44
CONECT   44   45   55  113
CONECT   45   46   54
CONECT   46   47   47  114
CONECT   47   48
CONECT   48   49   49   54
CONECT   49   50   51
CONECT   50  115  116
CONECT   51   52   52
CONECT   52   53  117
CONECT   53   54   54
CONECT   55   56   57  118
CONECT   56  119
CONECT   57   58  120
CONECT   58   59
CONECT   59   60   60   61   62
CONECT   61  121
CONECT   62  122
END
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SMILES for HMDB0013109 (Tridecanoyl-CoA)

CCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N
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INCHI for HMDB0013109 (Tridecanoyl-CoA)

InChI=1S/C34H60N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-25(43)62-18-17-36-24(42)15-16-37-32(46)29(45)34(2,3)20-55-61(52,53)58-60(50,51)54-19-23-28(57-59(47,48)49)27(44)33(56-23)41-22-40-26-30(35)38-21-39-31(26)41/h21-23,27-29,33,44-45H,4-20H2,1-3H3,(H,36,42)(H,37,46)(H,50,51)(H,52,53)(H2,35,38,39)(H2,47,48,49)/t23-,27-,28-,29?,33-/m1/s1
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
Tridecanoyl-coenzyme AHMDB
Tridecanoyl coenzyme AMeSH, HMDB
13-Iodotridecanoyl CoA, (125I)-labeledMeSH, HMDB
Tridecanoyl CoAMeSH, HMDB
Chemical FormulaC34H60N7O17P3S
Average Molecular Weight963.863
Monoisotopic Molecular Weight963.297923755
IUPAC Name{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-({[hydroxy({[hydroxy({3-hydroxy-2,2-dimethyl-3-[(2-{[2-(tridecanoylsulfanyl)ethyl]carbamoyl}ethyl)carbamoyl]propoxy})phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-3-yl]oxy}phosphonic acid
Traditional Name[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-2-({[hydroxy([hydroxy(3-hydroxy-2,2-dimethyl-3-[(2-{[2-(tridecanoylsulfanyl)ethyl]carbamoyl}ethyl)carbamoyl]propoxy)phosphoryl]oxy)phosphoryl]oxy}methyl)oxolan-3-yl]oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N
InChI Identifier
InChI=1S/C34H60N7O17P3S/c1-4-5-6-7-8-9-10-11-12-13-14-25(43)62-18-17-36-24(42)15-16-37-32(46)29(45)34(2,3)20-55-61(52,53)58-60(50,51)54-19-23-28(57-59(47,48)49)27(44)33(56-23)41-22-40-26-30(35)38-21-39-31(26)41/h21-23,27-29,33,44-45H,4-20H2,1-3H3,(H,36,42)(H,37,46)(H,50,51)(H,52,53)(H2,35,38,39)(H2,47,48,49)/t23-,27-,28-,29?,33-/m1/s1
InChI KeyTZKUYUHMJHEXOQ-XILBVEEWSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as long-chain fatty acyl coas. These are acyl CoAs where the group acylated to the coenzyme A moiety is a long aliphatic chain of 13 to 21 carbon atoms.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acyl thioesters
Direct ParentLong-chain fatty acyl CoAs
Alternative Parents
Substituents
  • Coenzyme a or derivatives
  • Purine ribonucleoside 3',5'-bisphosphate
  • Purine ribonucleoside bisphosphate
  • Purine ribonucleoside diphosphate
  • Ribonucleoside 3'-phosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Beta amino acid or derivatives
  • Glycosyl compound
  • N-glycosyl compound
  • 6-aminopurine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pentose monosaccharide
  • Imidazopyrimidine
  • Purine
  • Monoalkyl phosphate
  • Aminopyrimidine
  • Imidolactam
  • N-acyl-amine
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Monosaccharide
  • Pyrimidine
  • Alkyl phosphate
  • Fatty amide
  • Phosphoric acid ester
  • Tetrahydrofuran
  • Imidazole
  • Azole
  • Heteroaromatic compound
  • Carbothioic s-ester
  • Secondary alcohol
  • Thiocarboxylic acid ester
  • Carboxamide group
  • Secondary carboxylic acid amide
  • Amino acid or derivatives
  • Sulfenyl compound
  • Thiocarboxylic acid or derivatives
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Carboxylic acid derivative
  • Organosulfur compound
  • Organic oxygen compound
  • Hydrocarbon derivative
  • Carbonyl group
  • Organic nitrogen compound
  • Primary amine
  • Organopnictogen compound
  • Organic oxide
  • Organooxygen compound
  • Organonitrogen compound
  • Alcohol
  • Amine
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationRoute of exposureSource
Process
Naturally occurring process
Role
Biological roleIndustrial application
Physical Properties
StateSolid
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility2.43 g/LALOGPS
logP1.59ALOGPS
logP-0.74ChemAxon
logS-2.6ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.01ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count17ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area363.63 ŲChemAxon
Rotatable Bond Count31ChemAxon
Refractivity222.84 m³·mol⁻¹ChemAxon
Polarizability93.93 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+240.56630932474
DeepCCS[M-H]-238.91330932474
DeepCCS[M-2H]-273.19530932474
DeepCCS[M+Na]+246.88530932474
AllCCS[M+H]+283.332859911
AllCCS[M+H-H2O]+283.932859911
AllCCS[M+NH4]+282.732859911
AllCCS[M+Na]+282.532859911
AllCCS[M-H]-286.332859911
AllCCS[M+Na-2H]-291.832859911
AllCCS[M+HCOO]-297.932859911

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Measured using a Waters Acquity ultraperformance liquid chromatography (UPLC) ethylene-bridged hybrid (BEH) C18 column (100 mm × 2.1 mm; 1.7 μmparticle diameter). Predicted by Afia on May 17, 2022. Predicted by Afia on May 17, 2022.5.06 minutes32390414
Predicted by Siyang on May 30, 202212.9146 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20226.24 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid319.1 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid2500.5 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid125.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid174.6 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid159.6 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid180.2 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid482.3 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid641.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)933.0 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid926.6 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid605.1 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid874.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid352.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid328.4 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate286.6 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA89.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water150.1 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB029287
KNApSAcK IDNot Available
Chemspider ID35032575
KEGG Compound IDNot Available
BioCyc ID4812-TRIMETHYLTRIDECANOYL-COA
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound53481606
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDM03050
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  2. Watson AD: Thematic review series: systems biology approaches to metabolic and cardiovascular disorders. Lipidomics: a global approach to lipid analysis in biological systems. J Lipid Res. 2006 Oct;47(10):2101-11. Epub 2006 Aug 10. [PubMed:16902246 ]
  3. Sethi JK, Vidal-Puig AJ: Thematic review series: adipocyte biology. Adipose tissue function and plasticity orchestrate nutritional adaptation. J Lipid Res. 2007 Jun;48(6):1253-62. Epub 2007 Mar 20. [PubMed:17374880 ]
  4. Lingwood D, Simons K: Lipid rafts as a membrane-organizing principle. Science. 2010 Jan 1;327(5961):46-50. doi: 10.1126/science.1174621. [PubMed:20044567 ]
  5. Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Drager A, Mih N, Gatto F, Nilsson A, Preciat Gonzalez GA, Aurich MK, Prlic A, Sastry A, Danielsdottir AD, Heinken A, Noronha A, Rose PW, Burley SK, Fleming RMT, Nielsen J, Thiele I, Palsson BO: Recon3D enables a three-dimensional view of gene variation in human metabolism. Nat Biotechnol. 2018 Mar;36(3):272-281. doi: 10.1038/nbt.4072. Epub 2018 Feb 19. [PubMed:29457794 ]
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.

Enzymes

Enzyme Details
1. 3-ketoacyl-CoA thiolase, peroxisomal
General function:
Involved in transferase activity, transferring acyl groups other than amino-acyl groups
Specific function:
Not Available
Gene Name:
ACAA1
Uniprot ID:
P09110
Molecular weight:
34664.46
Enzyme Details
2. Peroxisomal acyl-coenzyme A oxidase 1
General function:
Involved in acyl-CoA dehydrogenase activity
Specific function:
Catalyzes the desaturation of acyl-CoAs to 2-trans-enoyl-CoAs. Isoform 1 shows highest activity against medium-chain fatty acyl-CoAs and activity decreases with increasing chain length. Isoform 2 is active against a much broader range of substrates and shows activity towards very long-chain acyl-CoAs. Isoform 2 is twice as active as isoform 1 against 16-hydroxy-palmitoyl-CoA and is 25% more active against 1,16-hexadecanodioyl-CoA.
Gene Name:
ACOX1
Uniprot ID:
Q15067
Molecular weight:
70135.205
Enzyme Details
3. Peroxisomal acyl-coenzyme A oxidase 2
General function:
Involved in acyl-CoA dehydrogenase activity
Specific function:
Oxidizes the CoA esters of the bile acid intermediates di- and tri-hydroxycholestanoic acids.
Gene Name:
ACOX2
Uniprot ID:
Q99424
Molecular weight:
76826.14
Enzyme Details
4. Peroxisomal acyl-coenzyme A oxidase 3
General function:
Involved in oxidoreductase activity, acting on the CH-CH group of donors
Specific function:
Oxidizes the CoA-esters of 2-methyl-branched fatty acids (By similarity).
Gene Name:
ACOX3
Uniprot ID:
O15254
Molecular weight:
69574.075
Enzyme Details
5. Peroxisomal bifunctional enzyme
General function:
Involved in oxidoreductase activity
Specific function:
Not Available
Gene Name:
EHHADH
Uniprot ID:
Q08426
Molecular weight:
69153.26
Enzyme Details
6. Peroxisomal multifunctional enzyme type 2
General function:
Involved in oxidoreductase activity
Specific function:
Bifunctional enzyme acting on the peroxisomal beta-oxidation pathway for fatty acids. Catalyzes the formation of 3-ketoacyl-CoA intermediates from both straight-chain and 2-methyl-branched-chain fatty acids.
Gene Name:
HSD17B4
Uniprot ID:
P51659
Molecular weight:
79685.715