Hmdb loader

Showing metabocard for Dodecanoyl-sn-glycero-3-phosphocholine (HMDB0240736)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesXML
Record Information
Version5.0
StatusDetected but not Quantified
Creation Date2020-11-01 18:42:41 UTC
Update Date2021-09-14 14:59:16 UTC
HMDB IDHMDB0240736
Secondary Accession NumbersNone
Metabolite Identification
Common NameDodecanoyl-sn-glycero-3-phosphocholine
DescriptionDodecanoyl-sn-glycero-3-phosphocholine belongs to the class of organic compounds known as 2-acyl-sn-glycero-3-phosphocholines. These are glycerophosphocholines in which the glycerol is esterified with a fatty acid at O-2 position, and linked at position 3 to a phosphocholine. Based on a literature review very few articles have been published on Dodecanoyl-sn-glycero-3-phosphocholine.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0240736 (Dodecanoyl-sn-glycero-3-phosphocholine)


  Mrv1652311012019422D          

 29 28  0  0  0  0            999 V2000
   -0.1741   -7.6369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5959   -7.3406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0074   -7.5628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6491   -8.0814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4190   -7.7851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0606   -8.3037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8305   -8.0074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4722   -8.5260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2421   -8.2296    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8837   -8.7482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6536   -8.4519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7820   -7.6369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2953   -8.9705    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0652   -8.6741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1935   -7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9634   -7.5628    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7068   -9.1927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4767   -8.8964    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1184   -9.4150    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   10.5997  -10.0566    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.6370   -8.7734    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   11.7600   -9.9336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5299   -9.6373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1715  -10.1559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.9415   -9.8595    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   14.7114   -9.5632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2378  -10.6295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6451   -9.0896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 26 28  1  0  0  0  0
 26 29  1  0  0  0  0
M  CHG  2  22  -1  26   1
M  END
Download

3D MOL for HMDB0240736 (Dodecanoyl-sn-glycero-3-phosphocholine)

HMDB0240736
     RDKit          3D
Dodecanoyl-sn-glycero-3-phosphocholine
 71 70  0  0  0  0  0  0  0  0999 V2000
   10.7641   -0.9919    0.1122 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0172    0.2103    0.6159 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5384   -0.0090    0.3427 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7251    1.1469    0.8171 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2531    0.9901    0.5883 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9734    0.8596   -0.8746 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4960    0.7056   -1.1573 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9683   -0.5182   -0.5051 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5218   -0.8133   -0.7173 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1187   -1.0039   -2.1614 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.3622   -0.7976    2.0898 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2046    0.0689    0.2687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3540   -1.0824    0.9473 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8387   -1.7114    1.1524 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.9767   -2.8742    0.1056 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.2604    0.4785    0.8613 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.3511    1.1951   -1.4988 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.9669   -1.2896   -1.3221 H   0  0  0  0  0  0  0  0  0  0  0  0
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  -10.5474    0.5133   -0.7366 H   0  0  0  0  0  0  0  0  0  0  0  0
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  -10.1359   -0.3008    0.8384 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.5765    2.2546   -1.3763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0654    0.6976   -2.2141 H   0  0  0  0  0  0  0  0  0  0  0  0
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 29 69  1  0
 29 70  1  0
 29 71  1  0
M  CHG  2  22  -1  26   1
M  END
Download

3D SDF for HMDB0240736 (Dodecanoyl-sn-glycero-3-phosphocholine)


  Mrv1652311012019422D          

 29 28  0  0  0  0            999 V2000
   -0.1741   -7.6369    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5959   -7.3406    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0074   -7.5628    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6491   -8.0814    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4190   -7.7851    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0606   -8.3037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8305   -8.0074    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4722   -8.5260    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2421   -8.2296    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8837   -8.7482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6536   -8.4519    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7820   -7.6369    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.2953   -8.9705    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0652   -8.6741    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1935   -7.8592    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9634   -7.5628    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7068   -9.1927    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   11.1184   -9.4150    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   10.5997  -10.0566    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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   11.7600   -9.9336    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.5299   -9.6373    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   13.9415   -9.8595    0.0000 N   0  3  0  0  0  0  0  0  0  0  0  0
   14.7114   -9.5632    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2378  -10.6295    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.6451   -9.0896    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
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  6  7  1  0  0  0  0
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  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
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 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 26 28  1  0  0  0  0
 26 29  1  0  0  0  0
M  CHG  2  22  -1  26   1
M  END
> <DATABASE_ID>
HMDB0240736

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCCCCC(=O)OC(CO)COP([O-])(=O)OCC[N+](C)(C)C

> <INCHI_IDENTIFIER>
InChI=1S/C20H42NO7P/c1-5-6-7-8-9-10-11-12-13-14-20(23)28-19(17-22)18-27-29(24,25)26-16-15-21(2,3)4/h19,22H,5-18H2,1-4H3

> <INCHI_KEY>
GLSCDHQUIDQFRP-UHFFFAOYSA-N

> <FORMULA>
C20H42NO7P

> <MOLECULAR_WEIGHT>
439.53

> <EXACT_MASS>
439.269889694

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
71

> <JCHEM_AVERAGE_POLARIZABILITY>
48.961325432251876

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2-{[2-(dodecanoyloxy)-3-hydroxypropyl phosphono]oxy}ethyl)trimethylazanium

> <ALOGPS_LOGP>
0.32

> <JCHEM_LOGP>
-0.5855321831384124

> <ALOGPS_LOGS>
-5.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.579258211672176

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8550617598182937

> <JCHEM_PKA_STRONGEST_BASIC>
-2.983758125699806

> <JCHEM_POLAR_SURFACE_AREA>
105.12000000000002

> <JCHEM_REFRACTIVITY>
123.86969999999997

> <JCHEM_ROTATABLE_BOND_COUNT>
20

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.90e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2-{[2-(dodecanoyloxy)-3-hydroxypropyl phosphono]oxy}ethyl)trimethylazanium

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0240736 (Dodecanoyl-sn-glycero-3-phosphocholine)

HMDB0240736
     RDKit          3D
Dodecanoyl-sn-glycero-3-phosphocholine
 71 70  0  0  0  0  0  0  0  0999 V2000
   10.7641   -0.9919    0.1122 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0172    0.2103    0.6159 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5384   -0.0090    0.3427 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7251    1.1469    0.8171 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.2531    0.9901    0.5883 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9734    0.8596   -0.8746 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4960    0.7056   -1.1573 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9683   -0.5182   -0.5051 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5218   -0.8133   -0.7173 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1187   -1.0039   -2.1614 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6298   -1.3223   -2.1718 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1020   -0.2011   -1.5676 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0094    1.0037   -1.9398 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9680   -0.4372   -0.5337 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7381    0.4733    0.1405 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2111    0.4925    1.5915 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3622   -0.7976    2.0898 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2046    0.0689    0.2687 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3540   -1.0824    0.9473 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8387   -1.7114    1.1524 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.9767   -2.8742    0.1056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8606   -2.5548    2.6743 O   0  0  0  0  0  1  0  0  0  0  0  0
   -6.1967   -0.8422    1.0377 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2604    0.4785    0.8613 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7024    0.9962    0.7934 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4747    0.4481   -0.2603 N   0  0  0  0  0  4  0  0  0  0  0  0
   -8.2419   -0.9303   -0.5503 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8894    0.5499    0.1441 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3511    1.1951   -1.4988 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7438   -1.7613    0.9297 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.8278   -0.7080   -0.1095 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2699   -1.4498   -0.7551 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3802    1.1037    0.0678 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.1890    0.3357    1.6964 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2173   -0.9267    0.8887 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4135   -0.1303   -0.7410 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9518    1.2764    1.9097 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.0939    2.1077    0.3545 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8784    0.1397    1.2078 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.7664    1.9253    0.9350 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5458    0.0279   -1.3697 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3207    1.8168   -1.3532 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3181    0.7504   -2.2505 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0115    1.6450   -0.7575 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0722   -0.3709    0.6133 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6346   -1.4024   -0.7117 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2942   -1.7647   -0.1857 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9410   -0.0244   -0.2024 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2520   -0.1046   -2.7692 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6982   -1.8712   -2.5394 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5050   -2.2199   -1.5461 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2849   -1.5488   -3.2048 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6850    1.4960   -0.2146 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7234    1.2522    2.1798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1108    0.6546    1.4874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5160   -1.3099    2.0897 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6489    0.9078    0.8413 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6246    0.0812   -0.7458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7861    0.7450   -0.1246 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8049    1.1139    1.6578 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6182    2.0959    0.6385 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1716    0.8159    1.7798 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2352   -1.0268   -1.0116 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9669   -1.2896   -1.3221 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2885   -1.5657    0.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5474    0.5133   -0.7366 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0592    1.5033    0.6843 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1359   -0.3008    0.8384 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3287    0.9867   -1.8818 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5765    2.2546   -1.3763 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0654    0.6976   -2.2141 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  2  0
 12 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 15 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  2  0
 20 22  1  0
 20 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 26 28  1  0
 26 29  1  0
  1 30  1  0
  1 31  1  0
  1 32  1  0
  2 33  1  0
  2 34  1  0
  3 35  1  0
  3 36  1  0
  4 37  1  0
  4 38  1  0
  5 39  1  0
  5 40  1  0
  6 41  1  0
  6 42  1  0
  7 43  1  0
  7 44  1  0
  8 45  1  0
  8 46  1  0
  9 47  1  0
  9 48  1  0
 10 49  1  0
 10 50  1  0
 11 51  1  0
 11 52  1  0
 15 53  1  0
 16 54  1  0
 16 55  1  0
 17 56  1  0
 18 57  1  0
 18 58  1  0
 24 59  1  0
 24 60  1  0
 25 61  1  0
 25 62  1  0
 27 63  1  0
 27 64  1  0
 27 65  1  0
 28 66  1  0
 28 67  1  0
 28 68  1  0
 29 69  1  0
 29 70  1  0
 29 71  1  0
M  CHG  2  22  -1  26   1
M  END
Download

PDB for HMDB0240736 (Dodecanoyl-sn-glycero-3-phosphocholine)

HEADER    PROTEIN                                 01-NOV-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   01-NOV-20         0                                  
HETATM    1  C   UNK     0      -0.325 -14.256   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.112 -13.702   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310 -14.670   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.747 -14.117   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.945 -15.085   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.382 -14.532   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.580 -15.500   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.017 -14.947   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      10.215 -15.915   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      11.652 -15.362   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      12.850 -16.330   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      14.287 -15.777   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      14.526 -14.256   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      15.484 -16.745   0.000  0.00  0.00           O+0
HETATM   15  C   UNK     0      16.922 -16.192   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      17.161 -14.670   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0      18.598 -14.117   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      18.119 -17.160   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      19.557 -16.607   0.000  0.00  0.00           O+0
HETATM   20  P   UNK     0      20.754 -17.575   0.000  0.00  0.00           P+0
HETATM   21  O   UNK     0      19.786 -18.772   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      21.722 -16.377   0.000  0.00  0.00           O-1
HETATM   23  O   UNK     0      21.952 -18.543   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      23.389 -17.990   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      24.587 -18.958   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0      26.024 -18.404   0.000  0.00  0.00           N+1
HETATM   27  C   UNK     0      27.461 -17.851   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      26.577 -19.842   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      25.471 -16.967   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15                                                       
CONECT   15   14   16   18                                                  
CONECT   16   15   17                                                       
CONECT   17   16                                                            
CONECT   18   15   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22   23                                             
CONECT   21   20                                                            
CONECT   22   20                                                            
CONECT   23   20   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27   28   29                                             
CONECT   27   26                                                            
CONECT   28   26                                                            
CONECT   29   26                                                            
MASTER        0    0    0    0    0    0    0    0   29    0   56    0
END
Download

3D PDB for HMDB0240736 (Dodecanoyl-sn-glycero-3-phosphocholine)

COMPND    HMDB0240736
HETATM    1  C1  UNL     1      10.764  -0.992   0.112  1.00  0.00           C  
HETATM    2  C2  UNL     1      10.017   0.210   0.616  1.00  0.00           C  
HETATM    3  C3  UNL     1       8.538  -0.009   0.343  1.00  0.00           C  
HETATM    4  C4  UNL     1       7.725   1.147   0.817  1.00  0.00           C  
HETATM    5  C5  UNL     1       6.253   0.990   0.588  1.00  0.00           C  
HETATM    6  C6  UNL     1       5.973   0.860  -0.875  1.00  0.00           C  
HETATM    7  C7  UNL     1       4.496   0.706  -1.157  1.00  0.00           C  
HETATM    8  C8  UNL     1       3.968  -0.518  -0.505  1.00  0.00           C  
HETATM    9  C9  UNL     1       2.522  -0.813  -0.717  1.00  0.00           C  
HETATM   10  C10 UNL     1       2.119  -1.004  -2.161  1.00  0.00           C  
HETATM   11  C11 UNL     1       0.630  -1.322  -2.172  1.00  0.00           C  
HETATM   12  C12 UNL     1      -0.102  -0.201  -1.568  1.00  0.00           C  
HETATM   13  O1  UNL     1       0.009   1.004  -1.940  1.00  0.00           O  
HETATM   14  O2  UNL     1      -0.968  -0.437  -0.534  1.00  0.00           O  
HETATM   15  C13 UNL     1      -1.738   0.473   0.141  1.00  0.00           C  
HETATM   16  C14 UNL     1      -1.211   0.492   1.591  1.00  0.00           C  
HETATM   17  O3  UNL     1      -1.362  -0.798   2.090  1.00  0.00           O  
HETATM   18  C15 UNL     1      -3.205   0.069   0.269  1.00  0.00           C  
HETATM   19  O4  UNL     1      -3.354  -1.082   0.947  1.00  0.00           O  
HETATM   20  P1  UNL     1      -4.839  -1.711   1.152  1.00  0.00           P  
HETATM   21  O5  UNL     1      -4.977  -2.874   0.106  1.00  0.00           O  
HETATM   22  O6  UNL     1      -4.861  -2.555   2.674  1.00  0.00           O1-
HETATM   23  O7  UNL     1      -6.197  -0.842   1.038  1.00  0.00           O  
HETATM   24  C16 UNL     1      -6.260   0.479   0.861  1.00  0.00           C  
HETATM   25  C17 UNL     1      -7.702   0.996   0.793  1.00  0.00           C  
HETATM   26  N1  UNL     1      -8.475   0.448  -0.260  1.00  0.00           N1+
HETATM   27  C18 UNL     1      -8.242  -0.930  -0.550  1.00  0.00           C  
HETATM   28  C19 UNL     1      -9.889   0.550   0.144  1.00  0.00           C  
HETATM   29  C20 UNL     1      -8.351   1.195  -1.499  1.00  0.00           C  
HETATM   30  H1  UNL     1      10.744  -1.761   0.930  1.00  0.00           H  
HETATM   31  H2  UNL     1      11.828  -0.708  -0.109  1.00  0.00           H  
HETATM   32  H3  UNL     1      10.270  -1.450  -0.755  1.00  0.00           H  
HETATM   33  H4  UNL     1      10.380   1.104   0.068  1.00  0.00           H  
HETATM   34  H5  UNL     1      10.189   0.336   1.696  1.00  0.00           H  
HETATM   35  H6  UNL     1       8.217  -0.927   0.889  1.00  0.00           H  
HETATM   36  H7  UNL     1       8.414  -0.130  -0.741  1.00  0.00           H  
HETATM   37  H8  UNL     1       7.952   1.276   1.910  1.00  0.00           H  
HETATM   38  H9  UNL     1       8.094   2.108   0.354  1.00  0.00           H  
HETATM   39  H10 UNL     1       5.878   0.140   1.208  1.00  0.00           H  
HETATM   40  H11 UNL     1       5.766   1.925   0.935  1.00  0.00           H  
HETATM   41  H12 UNL     1       6.546   0.028  -1.370  1.00  0.00           H  
HETATM   42  H13 UNL     1       6.321   1.817  -1.353  1.00  0.00           H  
HETATM   43  H14 UNL     1       4.318   0.750  -2.251  1.00  0.00           H  
HETATM   44  H15 UNL     1       4.011   1.645  -0.758  1.00  0.00           H  
HETATM   45  H16 UNL     1       4.072  -0.371   0.613  1.00  0.00           H  
HETATM   46  H17 UNL     1       4.635  -1.402  -0.712  1.00  0.00           H  
HETATM   47  H18 UNL     1       2.294  -1.765  -0.186  1.00  0.00           H  
HETATM   48  H19 UNL     1       1.941  -0.024  -0.202  1.00  0.00           H  
HETATM   49  H20 UNL     1       2.252  -0.105  -2.769  1.00  0.00           H  
HETATM   50  H21 UNL     1       2.698  -1.871  -2.539  1.00  0.00           H  
HETATM   51  H22 UNL     1       0.505  -2.220  -1.546  1.00  0.00           H  
HETATM   52  H23 UNL     1       0.285  -1.549  -3.205  1.00  0.00           H  
HETATM   53  H24 UNL     1      -1.685   1.496  -0.215  1.00  0.00           H  
HETATM   54  H25 UNL     1      -1.723   1.252   2.180  1.00  0.00           H  
HETATM   55  H26 UNL     1      -0.111   0.655   1.487  1.00  0.00           H  
HETATM   56  H27 UNL     1      -0.516  -1.310   2.090  1.00  0.00           H  
HETATM   57  H28 UNL     1      -3.649   0.908   0.841  1.00  0.00           H  
HETATM   58  H29 UNL     1      -3.625   0.081  -0.746  1.00  0.00           H  
HETATM   59  H30 UNL     1      -5.786   0.745  -0.125  1.00  0.00           H  
HETATM   60  H31 UNL     1      -5.805   1.114   1.658  1.00  0.00           H  
HETATM   61  H32 UNL     1      -7.618   2.096   0.639  1.00  0.00           H  
HETATM   62  H33 UNL     1      -8.172   0.816   1.780  1.00  0.00           H  
HETATM   63  H34 UNL     1      -7.235  -1.027  -1.012  1.00  0.00           H  
HETATM   64  H35 UNL     1      -8.967  -1.290  -1.322  1.00  0.00           H  
HETATM   65  H36 UNL     1      -8.289  -1.566   0.350  1.00  0.00           H  
HETATM   66  H37 UNL     1     -10.547   0.513  -0.737  1.00  0.00           H  
HETATM   67  H38 UNL     1     -10.059   1.503   0.684  1.00  0.00           H  
HETATM   68  H39 UNL     1     -10.136  -0.301   0.838  1.00  0.00           H  
HETATM   69  H40 UNL     1      -7.329   0.987  -1.882  1.00  0.00           H  
HETATM   70  H41 UNL     1      -8.576   2.255  -1.376  1.00  0.00           H  
HETATM   71  H42 UNL     1      -9.065   0.698  -2.214  1.00  0.00           H  
CONECT    1    2   30   31   32
CONECT    2    3   33   34
CONECT    3    4   35   36
CONECT    4    5   37   38
CONECT    5    6   39   40
CONECT    6    7   41   42
CONECT    7    8   43   44
CONECT    8    9   45   46
CONECT    9   10   47   48
CONECT   10   11   49   50
CONECT   11   12   51   52
CONECT   12   13   13   14
CONECT   14   15
CONECT   15   16   18   53
CONECT   16   17   54   55
CONECT   17   56
CONECT   18   19   57   58
CONECT   19   20
CONECT   20   21   21   22   23
CONECT   23   24
CONECT   24   25   59   60
CONECT   25   26   61   62
CONECT   26   27   28   29
CONECT   27   63   64   65
CONECT   28   66   67   68
CONECT   29   69   70   71
END
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SMILES for HMDB0240736 (Dodecanoyl-sn-glycero-3-phosphocholine)

CCCCCCCCCCCC(=O)OC(CO)COP([O-])(=O)OCC[N+](C)(C)C
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INCHI for HMDB0240736 (Dodecanoyl-sn-glycero-3-phosphocholine)

InChI=1S/C20H42NO7P/c1-5-6-7-8-9-10-11-12-13-14-20(23)28-19(17-22)18-27-29(24,25)26-16-15-21(2,3)4/h19,22H,5-18H2,1-4H3
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC20H42NO7P
Average Molecular Weight439.53
Monoisotopic Molecular Weight439.269889694
IUPAC Name(2-{[2-(dodecanoyloxy)-3-hydroxypropyl phosphono]oxy}ethyl)trimethylazanium
Traditional Name(2-{[2-(dodecanoyloxy)-3-hydroxypropyl phosphono]oxy}ethyl)trimethylazanium
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCC(=O)OC(CO)COP([O-])(=O)OCC[N+](C)(C)C
InChI Identifier
InChI=1S/C20H42NO7P/c1-5-6-7-8-9-10-11-12-13-14-20(23)28-19(17-22)18-27-29(24,25)26-16-15-21(2,3)4/h19,22H,5-18H2,1-4H3
InChI KeyGLSCDHQUIDQFRP-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 2-acyl-sn-glycero-3-phosphocholines. These are glycerophosphocholines in which the glycerol is esterified with a fatty acid at O-2 position, and linked at position 3 to a phosphocholine.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassGlycerophosphocholines
Direct Parent2-acyl-sn-glycero-3-phosphocholines
Alternative Parents
Substituents
  • 2-acyl-sn-glycero-3-phosphocholine
  • Phosphocholine
  • Choline
  • Fatty acid ester
  • Dialkyl phosphate
  • Organic phosphoric acid derivative
  • Fatty acyl
  • Phosphoric acid ester
  • Alkyl phosphate
  • Tetraalkylammonium salt
  • Quaternary ammonium salt
  • Carboxylic acid ester
  • Monocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Organic salt
  • Organooxygen compound
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organic oxide
  • Organic oxygen compound
  • Organic nitrogen compound
  • Carbonyl group
  • Amine
  • Alcohol
  • Primary alcohol
  • Organic cation
  • Aliphatic acyclic compound
Molecular FrameworkAliphatic acyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Biological locationSource
ProcessNot Available
RoleNot Available
Physical Properties
StateNot Available
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
logP0.32ALOGPS
logP-0.59ChemAxon
logS-5.4ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-3ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area105.12 ŲChemAxon
Rotatable Bond Count20ChemAxon
Refractivity123.87 m³·mol⁻¹ChemAxon
Polarizability48.96 ųChemAxon
Number of Rings0ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DeepCCS[M+H]+212.26230932474
DeepCCS[M-H]-208.24330932474
DeepCCS[M-2H]-244.78530932474
DeepCCS[M+Na]+221.07730932474

Predicted Retention Times

Underivatized

Chromatographic MethodRetention TimeReference
Predicted by Siyang on May 30, 202214.0511 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.74 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid2279.9 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid168.6 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid208.7 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid166.8 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid217.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid645.8 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 Acid615.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)599.7 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1507.4 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid479.6 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1845.2 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid356.1 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid417.0 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate252.4 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA70.1 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water31.5 seconds40023050

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
Dodecanoyl-sn-glycero-3-phosphocholineCCCCCCCCCCCC(=O)OC(CO)COP([O-])(=O)OCC[N+](C)(C)C3070.6Standard polar33892256
Dodecanoyl-sn-glycero-3-phosphocholineCCCCCCCCCCCC(=O)OC(CO)COP([O-])(=O)OCC[N+](C)(C)C2592.3Standard non polar33892256
Dodecanoyl-sn-glycero-3-phosphocholineCCCCCCCCCCCC(=O)OC(CO)COP([O-])(=O)OCC[N+](C)(C)C2821.0Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Dodecanoyl-sn-glycero-3-phosphocholine,1TMS,isomer #1CCCCCCCCCCCC(=O)OC(CO[Si](C)(C)C)COP(=O)([O-])OCC[N+](C)(C)C2886.3Semi standard non polar33892256
Dodecanoyl-sn-glycero-3-phosphocholine,1TBDMS,isomer #1CCCCCCCCCCCC(=O)OC(CO[Si](C)(C)C(C)(C)C)COP(=O)([O-])OCC[N+](C)(C)C3115.9Semi standard non polar33892256
Spectra
Biological Properties
Cellular LocationsNot Available
Biospecimen Locations
  • Blood
  • Urine
Tissue LocationsNot Available
Pathways
Normal Concentrations
BiospecimenStatusValueAgeSexConditionReferenceDetails
BloodDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
UrineDetected but not QuantifiedNot QuantifiedAdult (>18 years old)BothNormal details
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDNot Available
KNApSAcK IDNot Available
Chemspider ID8400702
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound10225211
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available