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Showing metabocard for Tomatine (HMDB0034103)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-11 18:53:48 UTC
Update Date2022-03-07 02:53:59 UTC
HMDB IDHMDB0034103
Secondary Accession Numbers
  • HMDB34103
Metabolite Identification
Common NameTomatine
DescriptionTomatine is a mildly toxic glycoalkaloid or glycospirosolane (steroidal alkaloids whose structure contains a spirosolane skeleton) found in the stems and leaves of tomato plants as well as in the fruit of unripened (green) tomatoes (up to 500 mg/kg). Red, ripe tomatoes have somewhat reduced amounts of tomatine. A toxic dose of tomatine for an adult human would appear to require the consumption of at least 500 g of tomato leaves in one sitting (“Toxic Plants of North America” (Iowa State University Press, 2001)). Tomatine is known to have fungicidal and antimicrobial properties and is likely produced by tomato plants as a defense against bacteria, fungi, viruses, and insects (PMID: 19514731 ). Some microbes produce an enzyme called tomatinase which can degrade tomatine, rendering it ineffective as an antimicrobial (PMID: 18835993 ).Tomatine has historically been used as a reagent in analytical chemistry for precipitating cholesterol from solution (PMID: 4362143 ). When lab animals ingest tomatine, essentially all of it passes through the animal unabsorbed. Tomatine apparently binds to cholesterol in the digestive tract, and the largely insoluble combination is excreted — ridding the body of both the alkaloid and cholesterol. Experiments with hamsters have shown that both tomatine-rich green tomatoes and purified tomatine can substantially lower the levels of undesirable LDL cholesterol while maintaining norma
Structure
Data?1563862511
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0034103 (Tomatine)


  Mrv0541 05061307342D          

 72 81  0  0  0  0            999 V2000
    2.5224   -0.8848    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4270    0.1094    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    6.6545   -0.2661    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.6277   -1.7905    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8476   -0.4631    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3768   -0.3192    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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 72 28  1  0  0  0  0
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M  END
Download

3D MOL for HMDB0034103 (Tomatine)

HMDB0034103
     RDKit          3D
Tomatine
155164  0  0  0  0  0  0  0  0999 V2000
   14.0042    1.1722   -0.5490 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7093   -0.2628   -0.1860 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9456   -0.9589   -1.2901 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5899   -0.3476   -1.3858 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8356   -0.3117   -0.1175 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5914    0.0864    1.0327 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.9215   -0.3926    1.0797 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1861   -1.5158    0.1982 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3074   -1.2006    1.2290 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0271   -2.0402    1.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2228   -1.1616    0.1953 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.0759   -2.2798    0.8145 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6811   -2.5575    0.2746 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9840   -1.2873   -0.1194 C   0  0  0  0  0  0  0  0  0  0  0  0
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    1.3910    0.3695    0.8895 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.7153   -0.4865    1.0135 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.8469   -0.3563    2.5233 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.1806   -0.5442   -1.0087 C   0  0  0  0  0  0  0  0  0  0  0  0
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    9.6082    0.6026   -0.2707 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0034103 (Tomatine)


  Mrv0541 05061307342D          

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M  END
> <DATABASE_ID>
HMDB0034103

> <DATABASE_NAME>
hmdb

> <SMILES>
CC1C2C(CC3C4CCC5CC(CCC5(C)C4CCC23C)OC2OC(CO)C(OC3OC(CO)C(O)C(OC4OCC(O)C(O)C4O)C3OC3OC(CO)C(O)C(O)C3O)C(O)C2O)OC11CCC(C)CN1

> <INCHI_IDENTIFIER>
InChI=1S/C50H83NO21/c1-20-7-12-50(51-15-20)21(2)32-28(72-50)14-26-24-6-5-22-13-23(8-10-48(22,3)25(24)9-11-49(26,32)4)65-45-40(63)37(60)41(31(18-54)68-45)69-47-43(71-46-39(62)36(59)34(57)29(16-52)66-46)42(35(58)30(17-53)67-47)70-44-38(61)33(56)27(55)19-64-44/h20-47,51-63H,5-19H2,1-4H3

> <INCHI_KEY>
REJLGAUYTKNVJM-UHFFFAOYSA-N

> <FORMULA>
C50H83NO21

> <MOLECULAR_WEIGHT>
1034.1881

> <EXACT_MASS>
1033.545758723

> <JCHEM_ACCEPTOR_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
110.87006564079888

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
13

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2-{[4,5-dihydroxy-2-(hydroxymethyl)-6-{5',7,9,13-tetramethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidine]oxy}oxan-3-yl]oxy}-5-hydroxy-6-(hydroxymethyl)-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-3-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-0.14

> <JCHEM_LOGP>
-1.4375506119999977

> <ALOGPS_LOGS>
-2.78

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
10

> <JCHEM_PHYSIOLOGICAL_CHARGE>
1

> <JCHEM_PKA>
12.226082035134647

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.779281985325843

> <JCHEM_PKA_STRONGEST_BASIC>
9.539133055650797

> <JCHEM_POLAR_SURFACE_AREA>
337.86000000000007

> <JCHEM_REFRACTIVITY>
244.78750000000008

> <JCHEM_ROTATABLE_BOND_COUNT>
11

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.71e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(2-{[4,5-dihydroxy-2-(hydroxymethyl)-6-{5',7,9,13-tetramethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidine]oxy}oxan-3-yl]oxy}-5-hydroxy-6-(hydroxymethyl)-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-3-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0034103 (Tomatine)

HMDB0034103
     RDKit          3D
Tomatine
155164  0  0  0  0  0  0  0  0999 V2000
   14.0042    1.1722   -0.5490 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7093   -0.2628   -0.1860 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.9456   -0.9589   -1.2901 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5899   -0.3476   -1.3858 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8356   -0.3117   -0.1175 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.5914    0.0864    1.0327 N   0  0  0  0  0  0  0  0  0  0  0  0
   12.9215   -0.3926    1.0797 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1861   -1.5158    0.1982 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3074   -1.2006    1.2290 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0271   -2.0402    1.0785 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2228   -1.1616    0.1953 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8975   -1.6098   -0.2449 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0759   -2.2798    0.8145 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6811   -2.5575    0.2746 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9840   -1.2873   -0.1194 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1273   -0.8998    1.0923 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3910    0.3695    0.8895 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.1060    0.1642    0.4199 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8759    0.5357    1.3092 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7728    1.4670    0.8810 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0165    1.0422    0.5167 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7832    2.3120    0.1034 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1385    2.9275   -0.9484 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8123    0.3619    1.6082 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7153   -0.4865    1.0135 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0506   -0.2083    1.2659 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5160   -1.3257    2.0004 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8735   -1.4824    1.9701 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2923   -1.9708    3.3661 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6829   -2.1472    3.3880 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6712   -0.2510    1.6937 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0055   -0.6657    1.4865 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2387    0.4641    0.4378 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0120    1.7906    0.8084 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7347    2.7121    0.0943 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6724    3.4168    0.8532 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4538    4.1182   -0.0950 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6384    5.3361   -0.4960 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9685    6.3446    0.4051 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1527    5.0685   -0.3553 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3861    5.8627   -1.2056 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8257    3.6217   -0.6694 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8747    3.4410   -2.0446 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8976   -0.1200    0.0385 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0624   -1.3581   -0.5860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7101   -1.3517   -1.9200 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8079   -1.7053   -2.6925 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4445   -2.8433   -2.2033 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4894   -3.2349   -3.2517 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4172   -2.2310   -3.4612 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5454   -4.0137   -1.9935 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5191   -4.8172   -3.1345 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1712   -3.6963   -1.5047 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2139   -3.5731   -0.1052 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6674   -2.4220   -2.1411 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5587   -2.6781   -3.5150 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8469   -0.3563    2.5233 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4389    0.5392    3.5170 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5972   -0.7297    1.7517 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9981   -1.4362    0.6352 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1051    1.3912    0.0886 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6233    1.1175    0.0664 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.7872   -0.1919   -0.6778 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1215    0.1598   -2.0465 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1806   -0.5442   -1.0087 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0854    0.6568   -1.2648 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7586    1.1974   -0.0683 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.3583    0.1750    0.8356 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8689    0.3160    2.2290 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8756    0.2487    0.9565 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6082    0.6026   -0.2707 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1148    2.0294   -0.2959 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5454    1.3702   -1.5372 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.0971    1.3381   -0.6812 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.5551    1.8779    0.1700 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.6869   -0.7715   -0.0016 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.4548   -0.8642   -2.2682 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.8168   -2.0263   -0.9976 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.6418    0.7008   -1.7914 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0088   -0.9160   -2.1426 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4086    1.0209    1.3966 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.9528   -1.4526    1.4056 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.4663    0.1761    1.8772 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7537   -1.3259    2.2154 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2575   -2.9870    0.5347 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5914   -2.3228    2.0334 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.8504   -1.0661   -0.7575 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1380   -2.4939   -0.9383 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5080   -3.2696    1.0593 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9700   -1.7466    1.7524 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0750   -3.0816    1.0355 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.7342   -3.2247   -0.6100 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2039   -1.5954   -0.8833 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5239   -1.7391    1.4400 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8914   -0.7262    1.9084 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2387    0.8042    1.9310 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4357    0.9440    2.2705 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9459    0.4252   -0.4025 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8380    2.1143   -0.0577 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6783    2.9945    0.9940 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7764    2.9697   -1.7036 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2950    1.1633    2.2110 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2369    0.6546    1.9021 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2072   -2.3258    1.2939 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0615   -1.1853    4.1148 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8219   -2.9344    3.6118 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9181   -3.0804    3.6686 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6518    0.3923    2.5960 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -8.9797    0.3854   -0.3835 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.3495    2.1384   -0.6526 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5819    3.4394   -0.9852 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.4263    4.3662    0.3347 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.7956    5.2748    0.6786 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5587    6.8173   -1.1096 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7541    3.4977   -0.3596 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4857    4.1263   -2.4047 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.5057    0.5536   -0.7514 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3628   -0.3558   -2.2683 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0347   -2.5950   -1.2768 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9773   -3.5457   -4.1966 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9858   -4.1564   -2.8711 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.0917   -1.5299   -4.0543 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0284   -4.6387   -1.1863 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0112   -5.6631   -3.0130 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5151   -4.5555   -1.7857 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2289   -4.4376    0.3449 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.7851    1.5529   -0.9334 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0354    2.3790    0.6224 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9391    1.1198    1.0968 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0120    1.9193   -0.5824 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6748   -0.3793   -2.8703 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0643   -0.0767   -2.0557 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2599    1.2273   -2.2752 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1067   -0.9663   -2.0702 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4918    1.4274   -1.7570 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8944    0.3934   -2.0115 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1282    1.8907    0.5252 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.6225    1.8482   -0.4056 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8254    0.6442    2.3588 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4620    1.1742    2.6816 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1377   -0.5352    2.8910 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1841    0.8819    1.8127 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1559    0.3905   -1.2315 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.7639    2.5657   -1.2257 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6895    2.5890    0.5531 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2240    2.0836   -0.3357 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
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M  END
Download

PDB for HMDB0034103 (Tomatine)

HEADER    PROTEIN                                 06-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-MAY-13         0                                  
HETATM    1  C   UNK     0       4.708  -1.652   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      10.130   0.204   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      17.174  -0.685   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      12.422  -0.497   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      17.710  -4.724   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      16.173  -4.635   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.772  -3.342   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      20.249  -0.864   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      15.637  -0.596   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      18.711  -0.775   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      14.099  -0.506   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       8.291  -3.592   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      20.094  -3.527   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      12.849  -4.252   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       7.204  -0.710   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      27.865  10.716   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      30.319  -0.115   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      22.787   2.996   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      34.395   3.656   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.228  -1.901   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      10.363  -1.318   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      18.556  -3.438   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      20.940  -2.241   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      15.482  -3.259   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      16.328  -1.972   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      13.944  -3.169   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      35.242   4.943   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      11.481  -3.545   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      28.556   9.339   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      29.628   1.261   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      23.479   1.620   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      11.731  -2.025   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      34.550   6.319   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      30.093   9.250   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      30.474   2.548   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      30.784   7.874   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      25.707   0.154   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      33.013   6.408   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      29.938   6.587   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      24.861  -1.133   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      25.016   1.530   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      29.783   3.924   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      28.246   4.014   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      32.167   5.122   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      23.324  -1.043   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      28.401   6.677   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      27.400   2.727   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      17.865  -2.062   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      13.253  -1.793   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       9.267  -2.401   0.000  0.00  0.00           C+0
HETATM   51  N   UNK     0       8.724  -0.960   0.000  0.00  0.00           N+0
HETATM   52  O   UNK     0      26.327  10.805   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      31.857  -0.204   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      21.250   3.085   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      36.779   4.853   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      35.397   7.605   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      30.939  10.537   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      32.012   2.459   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      32.322   7.784   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      27.245   0.064   0.000  0.00  0.00           O+0
HETATM   61  O   UNK     0      33.263   7.928   0.000  0.00  0.00           O+0
HETATM   62  O   UNK     0      31.306   5.880   0.000  0.00  0.00           O+0
HETATM   63  O   UNK     0      25.552  -2.509   0.000  0.00  0.00           O+0
HETATM   64  O   UNK     0      32.858   3.745   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      22.477  -2.330   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      27.710   8.053   0.000  0.00  0.00           O+0
HETATM   67  O   UNK     0      28.091   1.351   0.000  0.00  0.00           O+0
HETATM   68  O   UNK     0      22.632   0.333   0.000  0.00  0.00           O+0
HETATM   69  O   UNK     0      25.862   2.817   0.000  0.00  0.00           O+0
HETATM   70  O   UNK     0      30.629   5.211   0.000  0.00  0.00           O+0
HETATM   71  O   UNK     0      27.555   5.390   0.000  0.00  0.00           O+0
HETATM   72  O   UNK     0       9.958  -3.777   0.000  0.00  0.00           O+0
CONECT    1   20                                                            
CONECT    2   21                                                            
CONECT    3   48                                                            
CONECT    4   49                                                            
CONECT    5    6   22                                                       
CONECT    6    5   24                                                       
CONECT    7   12   20                                                       
CONECT    8   10   23                                                       
CONECT    9   11   25                                                       
CONECT   10    8   48                                                       
CONECT   11    9   49                                                       
CONECT   12    7   50                                                       
CONECT   13   22   23                                                       
CONECT   14   26   28                                                       
CONECT   15   20   51                                                       
CONECT   16   29   52                                                       
CONECT   17   30   53                                                       
CONECT   18   31   54                                                       
CONECT   19   27   64                                                       
CONECT   20    1    7   15                                                  
CONECT   21    2   32   50                                                  
CONECT   22    5   13   48                                                  
CONECT   23    8   13   65                                                  
CONECT   24    6   25   26                                                  
CONECT   25    9   24   48                                                  
CONECT   26   14   24   49                                                  
CONECT   27   19   33   55                                                  
CONECT   28   14   32   72                                                  
CONECT   29   16   34   66                                                  
CONECT   30   17   35   67                                                  
CONECT   31   18   41   68                                                  
CONECT   32   21   28   49                                                  
CONECT   33   27   38   56                                                  
CONECT   34   29   36   57                                                  
CONECT   35   30   42   58                                                  
CONECT   36   34   39   59                                                  
CONECT   37   40   41   60                                                  
CONECT   38   33   44   61                                                  
CONECT   39   36   46   62                                                  
CONECT   40   37   45   63                                                  
CONECT   41   31   37   69                                                  
CONECT   42   35   43   70                                                  
CONECT   43   42   47   71                                                  
CONECT   44   38   64   70                                                  
CONECT   45   40   65   68                                                  
CONECT   46   39   66   71                                                  
CONECT   47   43   67   69                                                  
CONECT   48    3   10   22   25                                             
CONECT   49    4   11   26   32                                             
CONECT   50   12   21   51   72                                             
CONECT   51   15   50                                                       
CONECT   52   16                                                            
CONECT   53   17                                                            
CONECT   54   18                                                            
CONECT   55   27                                                            
CONECT   56   33                                                            
CONECT   57   34                                                            
CONECT   58   35                                                            
CONECT   59   36                                                            
CONECT   60   37                                                            
CONECT   61   38                                                            
CONECT   62   39                                                            
CONECT   63   40                                                            
CONECT   64   19   44                                                       
CONECT   65   23   45                                                       
CONECT   66   29   46                                                       
CONECT   67   30   47                                                       
CONECT   68   31   45                                                       
CONECT   69   41   47                                                       
CONECT   70   42   44                                                       
CONECT   71   43   46                                                       
CONECT   72   28   50                                                       
MASTER        0    0    0    0    0    0    0    0   72    0  162    0
END
Download

3D PDB for HMDB0034103 (Tomatine)

COMPND    HMDB0034103
HETATM    1  C1  UNL     1      14.004   1.172  -0.549  1.00  0.00           C  
HETATM    2  C2  UNL     1      13.709  -0.263  -0.186  1.00  0.00           C  
HETATM    3  C3  UNL     1      12.946  -0.959  -1.290  1.00  0.00           C  
HETATM    4  C4  UNL     1      11.590  -0.348  -1.386  1.00  0.00           C  
HETATM    5  C5  UNL     1      10.836  -0.312  -0.117  1.00  0.00           C  
HETATM    6  N1  UNL     1      11.591   0.086   1.033  1.00  0.00           N  
HETATM    7  C6  UNL     1      12.922  -0.393   1.080  1.00  0.00           C  
HETATM    8  O1  UNL     1      10.186  -1.516   0.198  1.00  0.00           O  
HETATM    9  C7  UNL     1       9.307  -1.201   1.229  1.00  0.00           C  
HETATM   10  C8  UNL     1       8.027  -2.040   1.079  1.00  0.00           C  
HETATM   11  C9  UNL     1       7.223  -1.162   0.195  1.00  0.00           C  
HETATM   12  C10 UNL     1       5.897  -1.610  -0.245  1.00  0.00           C  
HETATM   13  C11 UNL     1       5.076  -2.280   0.815  1.00  0.00           C  
HETATM   14  C12 UNL     1       3.681  -2.558   0.275  1.00  0.00           C  
HETATM   15  C13 UNL     1       2.984  -1.287  -0.119  1.00  0.00           C  
HETATM   16  C14 UNL     1       2.127  -0.900   1.092  1.00  0.00           C  
HETATM   17  C15 UNL     1       1.391   0.369   0.889  1.00  0.00           C  
HETATM   18  O2  UNL     1       0.106   0.164   0.420  1.00  0.00           O  
HETATM   19  C16 UNL     1      -0.876   0.536   1.309  1.00  0.00           C  
HETATM   20  O3  UNL     1      -1.773   1.467   0.881  1.00  0.00           O  
HETATM   21  C17 UNL     1      -3.016   1.042   0.517  1.00  0.00           C  
HETATM   22  C18 UNL     1      -3.783   2.312   0.103  1.00  0.00           C  
HETATM   23  O4  UNL     1      -3.139   2.928  -0.948  1.00  0.00           O  
HETATM   24  C19 UNL     1      -3.812   0.362   1.608  1.00  0.00           C  
HETATM   25  O5  UNL     1      -4.715  -0.487   1.013  1.00  0.00           O  
HETATM   26  C20 UNL     1      -6.051  -0.208   1.266  1.00  0.00           C  
HETATM   27  O6  UNL     1      -6.516  -1.326   2.000  1.00  0.00           O  
HETATM   28  C21 UNL     1      -7.874  -1.482   1.970  1.00  0.00           C  
HETATM   29  C22 UNL     1      -8.292  -1.971   3.366  1.00  0.00           C  
HETATM   30  O7  UNL     1      -9.683  -2.147   3.388  1.00  0.00           O  
HETATM   31  C23 UNL     1      -8.671  -0.251   1.694  1.00  0.00           C  
HETATM   32  O8  UNL     1     -10.005  -0.666   1.486  1.00  0.00           O  
HETATM   33  C24 UNL     1      -8.239   0.464   0.438  1.00  0.00           C  
HETATM   34  O9  UNL     1      -8.012   1.791   0.808  1.00  0.00           O  
HETATM   35  C25 UNL     1      -8.735   2.712   0.094  1.00  0.00           C  
HETATM   36  O10 UNL     1      -9.672   3.417   0.853  1.00  0.00           O  
HETATM   37  C26 UNL     1     -10.454   4.118  -0.095  1.00  0.00           C  
HETATM   38  C27 UNL     1      -9.638   5.336  -0.496  1.00  0.00           C  
HETATM   39  O11 UNL     1      -9.969   6.345   0.405  1.00  0.00           O  
HETATM   40  C28 UNL     1      -8.153   5.069  -0.355  1.00  0.00           C  
HETATM   41  O12 UNL     1      -7.386   5.863  -1.206  1.00  0.00           O  
HETATM   42  C29 UNL     1      -7.826   3.622  -0.669  1.00  0.00           C  
HETATM   43  O13 UNL     1      -7.875   3.441  -2.045  1.00  0.00           O  
HETATM   44  C30 UNL     1      -6.898  -0.120   0.039  1.00  0.00           C  
HETATM   45  O14 UNL     1      -7.062  -1.358  -0.586  1.00  0.00           O  
HETATM   46  C31 UNL     1      -6.710  -1.352  -1.920  1.00  0.00           C  
HETATM   47  O15 UNL     1      -7.808  -1.705  -2.693  1.00  0.00           O  
HETATM   48  C32 UNL     1      -8.444  -2.843  -2.203  1.00  0.00           C  
HETATM   49  C33 UNL     1      -9.489  -3.235  -3.252  1.00  0.00           C  
HETATM   50  O16 UNL     1     -10.417  -2.231  -3.461  1.00  0.00           O  
HETATM   51  C34 UNL     1      -7.545  -4.014  -1.994  1.00  0.00           C  
HETATM   52  O17 UNL     1      -7.519  -4.817  -3.135  1.00  0.00           O  
HETATM   53  C35 UNL     1      -6.171  -3.696  -1.505  1.00  0.00           C  
HETATM   54  O18 UNL     1      -6.214  -3.573  -0.105  1.00  0.00           O  
HETATM   55  C36 UNL     1      -5.667  -2.422  -2.141  1.00  0.00           C  
HETATM   56  O19 UNL     1      -5.559  -2.678  -3.515  1.00  0.00           O  
HETATM   57  C37 UNL     1      -2.847  -0.356   2.523  1.00  0.00           C  
HETATM   58  O20 UNL     1      -2.439   0.539   3.517  1.00  0.00           O  
HETATM   59  C38 UNL     1      -1.597  -0.730   1.752  1.00  0.00           C  
HETATM   60  O21 UNL     1      -1.998  -1.436   0.635  1.00  0.00           O  
HETATM   61  C39 UNL     1       2.105   1.391   0.089  1.00  0.00           C  
HETATM   62  C40 UNL     1       3.623   1.117   0.066  1.00  0.00           C  
HETATM   63  C41 UNL     1       3.787  -0.192  -0.678  1.00  0.00           C  
HETATM   64  C42 UNL     1       3.122   0.160  -2.046  1.00  0.00           C  
HETATM   65  C43 UNL     1       5.181  -0.544  -1.009  1.00  0.00           C  
HETATM   66  C44 UNL     1       6.085   0.657  -1.265  1.00  0.00           C  
HETATM   67  C45 UNL     1       6.759   1.197  -0.068  1.00  0.00           C  
HETATM   68  C46 UNL     1       7.358   0.175   0.836  1.00  0.00           C  
HETATM   69  C47 UNL     1       6.869   0.316   2.229  1.00  0.00           C  
HETATM   70  C48 UNL     1       8.876   0.249   0.957  1.00  0.00           C  
HETATM   71  C49 UNL     1       9.608   0.603  -0.271  1.00  0.00           C  
HETATM   72  C50 UNL     1      10.115   2.029  -0.296  1.00  0.00           C  
HETATM   73  H1  UNL     1      13.545   1.370  -1.537  1.00  0.00           H  
HETATM   74  H2  UNL     1      15.097   1.338  -0.681  1.00  0.00           H  
HETATM   75  H3  UNL     1      13.555   1.878   0.170  1.00  0.00           H  
HETATM   76  H4  UNL     1      14.687  -0.772  -0.002  1.00  0.00           H  
HETATM   77  H5  UNL     1      13.455  -0.864  -2.268  1.00  0.00           H  
HETATM   78  H6  UNL     1      12.817  -2.026  -0.998  1.00  0.00           H  
HETATM   79  H7  UNL     1      11.642   0.701  -1.791  1.00  0.00           H  
HETATM   80  H8  UNL     1      11.009  -0.916  -2.143  1.00  0.00           H  
HETATM   81  H9  UNL     1      11.409   1.021   1.397  1.00  0.00           H  
HETATM   82  H10 UNL     1      12.953  -1.453   1.406  1.00  0.00           H  
HETATM   83  H11 UNL     1      13.466   0.176   1.877  1.00  0.00           H  
HETATM   84  H12 UNL     1       9.754  -1.326   2.215  1.00  0.00           H  
HETATM   85  H13 UNL     1       8.258  -2.987   0.535  1.00  0.00           H  
HETATM   86  H14 UNL     1       7.591  -2.323   2.033  1.00  0.00           H  
HETATM   87  H15 UNL     1       7.850  -1.066  -0.758  1.00  0.00           H  
HETATM   88  H16 UNL     1       6.138  -2.494  -0.938  1.00  0.00           H  
HETATM   89  H17 UNL     1       5.508  -3.270   1.059  1.00  0.00           H  
HETATM   90  H18 UNL     1       4.970  -1.747   1.752  1.00  0.00           H  
HETATM   91  H19 UNL     1       3.075  -3.082   1.035  1.00  0.00           H  
HETATM   92  H20 UNL     1       3.734  -3.225  -0.610  1.00  0.00           H  
HETATM   93  H21 UNL     1       2.204  -1.595  -0.883  1.00  0.00           H  
HETATM   94  H22 UNL     1       1.524  -1.739   1.440  1.00  0.00           H  
HETATM   95  H23 UNL     1       2.891  -0.726   1.908  1.00  0.00           H  
HETATM   96  H24 UNL     1       1.239   0.804   1.931  1.00  0.00           H  
HETATM   97  H25 UNL     1      -0.436   0.944   2.270  1.00  0.00           H  
HETATM   98  H26 UNL     1      -2.946   0.425  -0.403  1.00  0.00           H  
HETATM   99  H27 UNL     1      -4.838   2.114  -0.058  1.00  0.00           H  
HETATM  100  H28 UNL     1      -3.678   2.994   0.994  1.00  0.00           H  
HETATM  101  H29 UNL     1      -3.776   2.970  -1.704  1.00  0.00           H  
HETATM  102  H30 UNL     1      -4.295   1.163   2.211  1.00  0.00           H  
HETATM  103  H31 UNL     1      -6.237   0.655   1.902  1.00  0.00           H  
HETATM  104  H32 UNL     1      -8.207  -2.326   1.294  1.00  0.00           H  
HETATM  105  H33 UNL     1      -8.061  -1.185   4.115  1.00  0.00           H  
HETATM  106  H34 UNL     1      -7.822  -2.934   3.612  1.00  0.00           H  
HETATM  107  H35 UNL     1      -9.918  -3.080   3.669  1.00  0.00           H  
HETATM  108  H36 UNL     1      -8.652   0.392   2.596  1.00  0.00           H  
HETATM  109  H37 UNL     1     -10.548   0.121   1.216  1.00  0.00           H  
HETATM  110  H38 UNL     1      -8.980   0.385  -0.383  1.00  0.00           H  
HETATM  111  H39 UNL     1      -9.350   2.138  -0.653  1.00  0.00           H  
HETATM  112  H40 UNL     1     -10.582   3.439  -0.985  1.00  0.00           H  
HETATM  113  H41 UNL     1     -11.426   4.366   0.335  1.00  0.00           H  
HETATM  114  H42 UNL     1      -9.870   5.600  -1.548  1.00  0.00           H  
HETATM  115  H43 UNL     1     -10.792   6.145   0.928  1.00  0.00           H  
HETATM  116  H44 UNL     1      -7.796   5.275   0.679  1.00  0.00           H  
HETATM  117  H45 UNL     1      -7.559   6.817  -1.110  1.00  0.00           H  
HETATM  118  H46 UNL     1      -6.754   3.498  -0.360  1.00  0.00           H  
HETATM  119  H47 UNL     1      -8.486   4.126  -2.405  1.00  0.00           H  
HETATM  120  H48 UNL     1      -6.506   0.554  -0.751  1.00  0.00           H  
HETATM  121  H49 UNL     1      -6.363  -0.356  -2.268  1.00  0.00           H  
HETATM  122  H50 UNL     1      -9.035  -2.595  -1.277  1.00  0.00           H  
HETATM  123  H51 UNL     1      -8.977  -3.546  -4.197  1.00  0.00           H  
HETATM  124  H52 UNL     1      -9.986  -4.156  -2.871  1.00  0.00           H  
HETATM  125  H53 UNL     1     -10.092  -1.530  -4.054  1.00  0.00           H  
HETATM  126  H54 UNL     1      -8.028  -4.639  -1.186  1.00  0.00           H  
HETATM  127  H55 UNL     1      -8.011  -5.663  -3.013  1.00  0.00           H  
HETATM  128  H56 UNL     1      -5.515  -4.555  -1.786  1.00  0.00           H  
HETATM  129  H57 UNL     1      -6.229  -4.438   0.345  1.00  0.00           H  
HETATM  130  H58 UNL     1      -4.681  -2.119  -1.715  1.00  0.00           H  
HETATM  131  H59 UNL     1      -5.287  -3.637  -3.642  1.00  0.00           H  
HETATM  132  H60 UNL     1      -3.246  -1.242   3.008  1.00  0.00           H  
HETATM  133  H61 UNL     1      -2.272   1.451   3.167  1.00  0.00           H  
HETATM  134  H62 UNL     1      -0.985  -1.361   2.402  1.00  0.00           H  
HETATM  135  H63 UNL     1      -2.148  -2.402   0.799  1.00  0.00           H  
HETATM  136  H64 UNL     1       1.785   1.553  -0.933  1.00  0.00           H  
HETATM  137  H65 UNL     1       2.035   2.379   0.622  1.00  0.00           H  
HETATM  138  H66 UNL     1       3.939   1.120   1.097  1.00  0.00           H  
HETATM  139  H67 UNL     1       4.012   1.919  -0.582  1.00  0.00           H  
HETATM  140  H68 UNL     1       3.675  -0.379  -2.870  1.00  0.00           H  
HETATM  141  H69 UNL     1       2.064  -0.077  -2.056  1.00  0.00           H  
HETATM  142  H70 UNL     1       3.260   1.227  -2.275  1.00  0.00           H  
HETATM  143  H71 UNL     1       5.107  -0.966  -2.070  1.00  0.00           H  
HETATM  144  H72 UNL     1       5.492   1.427  -1.757  1.00  0.00           H  
HETATM  145  H73 UNL     1       6.894   0.393  -2.011  1.00  0.00           H  
HETATM  146  H74 UNL     1       6.128   1.891   0.525  1.00  0.00           H  
HETATM  147  H75 UNL     1       7.623   1.848  -0.406  1.00  0.00           H  
HETATM  148  H76 UNL     1       5.825   0.644   2.359  1.00  0.00           H  
HETATM  149  H77 UNL     1       7.462   1.174   2.682  1.00  0.00           H  
HETATM  150  H78 UNL     1       7.138  -0.535   2.891  1.00  0.00           H  
HETATM  151  H79 UNL     1       9.184   0.882   1.813  1.00  0.00           H  
HETATM  152  H80 UNL     1       9.156   0.390  -1.231  1.00  0.00           H  
HETATM  153  H81 UNL     1       9.764   2.566  -1.226  1.00  0.00           H  
HETATM  154  H82 UNL     1       9.689   2.589   0.553  1.00  0.00           H  
HETATM  155  H83 UNL     1      11.224   2.084  -0.336  1.00  0.00           H  
CONECT    1    2   73   74   75
CONECT    2    3    7   76
CONECT    3    4   77   78
CONECT    4    5   79   80
CONECT    5    6    8   71
CONECT    6    7   81
CONECT    7   82   83
CONECT    8    9
CONECT    9   10   70   84
CONECT   10   11   85   86
CONECT   11   12   68   87
CONECT   12   13   65   88
CONECT   13   14   89   90
CONECT   14   15   91   92
CONECT   15   16   63   93
CONECT   16   17   94   95
CONECT   17   18   61   96
CONECT   18   19
CONECT   19   20   59   97
CONECT   20   21
CONECT   21   22   24   98
CONECT   22   23   99  100
CONECT   23  101
CONECT   24   25   57  102
CONECT   25   26
CONECT   26   27   44  103
CONECT   27   28
CONECT   28   29   31  104
CONECT   29   30  105  106
CONECT   30  107
CONECT   31   32   33  108
CONECT   32  109
CONECT   33   34   44  110
CONECT   34   35
CONECT   35   36   42  111
CONECT   36   37
CONECT   37   38  112  113
CONECT   38   39   40  114
CONECT   39  115
CONECT   40   41   42  116
CONECT   41  117
CONECT   42   43  118
CONECT   43  119
CONECT   44   45  120
CONECT   45   46
CONECT   46   47   55  121
CONECT   47   48
CONECT   48   49   51  122
CONECT   49   50  123  124
CONECT   50  125
CONECT   51   52   53  126
CONECT   52  127
CONECT   53   54   55  128
CONECT   54  129
CONECT   55   56  130
CONECT   56  131
CONECT   57   58   59  132
CONECT   58  133
CONECT   59   60  134
CONECT   60  135
CONECT   61   62  136  137
CONECT   62   63  138  139
CONECT   63   64   65
CONECT   64  140  141  142
CONECT   65   66  143
CONECT   66   67  144  145
CONECT   67   68  146  147
CONECT   68   69   70
CONECT   69  148  149  150
CONECT   70   71  151
CONECT   71   72  152
CONECT   72  153  154  155
END
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SMILES for HMDB0034103 (Tomatine)

CC1C2C(CC3C4CCC5CC(CCC5(C)C4CCC23C)OC2OC(CO)C(OC3OC(CO)C(O)C(OC4OCC(O)C(O)C4O)C3OC3OC(CO)C(O)C(O)C3O)C(O)C2O)OC11CCC(C)CN1
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INCHI for HMDB0034103 (Tomatine)

InChI=1S/C50H83NO21/c1-20-7-12-50(51-15-20)21(2)32-28(72-50)14-26-24-6-5-22-13-23(8-10-48(22,3)25(24)9-11-49(26,32)4)65-45-40(63)37(60)41(31(18-54)68-45)69-47-43(71-46-39(62)36(59)34(57)29(16-52)66-46)42(35(58)30(17-53)67-47)70-44-38(61)33(56)27(55)19-64-44/h20-47,51-63H,5-19H2,1-4H3
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View in JSmolView NMR AssignmentsView Stereo Labels
Synonyms
ValueSource
A''-tomatidineHMDB
a-TomatineHMDB
alpha -TomatineHMDB
alpha-TomatineHMDB
LycopersicinHMDB
Tomatidine, glycosideHMDB
TomatinHMDB
TomatineMeSH
Chemical FormulaC50H83NO21
Average Molecular Weight1034.1881
Monoisotopic Molecular Weight1033.545758723
IUPAC Name2-[(2-{[4,5-dihydroxy-2-(hydroxymethyl)-6-{5',7,9,13-tetramethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidine]oxy}oxan-3-yl]oxy}-5-hydroxy-6-(hydroxymethyl)-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-3-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional Name2-[(2-{[4,5-dihydroxy-2-(hydroxymethyl)-6-{5',7,9,13-tetramethyl-5-oxaspiro[pentacyclo[10.8.0.0²,⁹.0⁴,⁸.0¹³,¹⁸]icosane-6,2'-piperidine]oxy}oxan-3-yl]oxy}-5-hydroxy-6-(hydroxymethyl)-4-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-3-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol
CAS Registry Number17406-45-0
SMILES
CC1C2C(CC3C4CCC5CC(CCC5(C)C4CCC23C)OC2OC(CO)C(OC3OC(CO)C(O)C(OC4OCC(O)C(O)C4O)C3OC3OC(CO)C(O)C(O)C3O)C(O)C2O)OC11CCC(C)CN1
InChI Identifier
InChI=1S/C50H83NO21/c1-20-7-12-50(51-15-20)21(2)32-28(72-50)14-26-24-6-5-22-13-23(8-10-48(22,3)25(24)9-11-49(26,32)4)65-45-40(63)37(60)41(31(18-54)68-45)69-47-43(71-46-39(62)36(59)34(57)29(16-52)66-46)42(35(58)30(17-53)67-47)70-44-38(61)33(56)27(55)19-64-44/h20-47,51-63H,5-19H2,1-4H3
InChI KeyREJLGAUYTKNVJM-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as steroidal saponins. These are saponins in which the aglycone moiety is a steroid. The steroidal aglycone is usually a spirostane, furostane, spirosolane, solanidane, or curcubitacin derivative.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassSteroids and steroid derivatives
Sub ClassSteroidal glycosides
Direct ParentSteroidal saponins
Alternative Parents
Substituents
  • Steroidal saponin
  • Diterpene glycoside
  • Spirosolane skeleton
  • Oligosaccharide
  • Diterpenoid
  • Steroidal alkaloid
  • Azasteroid
  • Terpene glycoside
  • Glycosyl compound
  • O-glycosyl compound
  • Azaspirodecane
  • Alkaloid or derivatives
  • Oxane
  • Piperidine
  • Tetrahydrofuran
  • Secondary alcohol
  • Hemiaminal
  • Polyol
  • Secondary amine
  • Acetal
  • Secondary aliphatic amine
  • Oxacycle
  • Organoheterocyclic compound
  • Azacycle
  • Primary alcohol
  • Organonitrogen compound
  • Hydrocarbon derivative
  • Organopnictogen compound
  • Organooxygen compound
  • Organic oxygen compound
  • Organic nitrogen compound
  • Amine
  • Alcohol
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic 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 Point263 - 267 °CNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility1.71 g/LALOGPS
logP-0.14ALOGPS
logP-1.4ChemAxon
logS-2.8ALOGPS
pKa (Strongest Acidic)11.78ChemAxon
pKa (Strongest Basic)9.54ChemAxon
Physiological Charge1ChemAxon
Hydrogen Acceptor Count22ChemAxon
Hydrogen Donor Count13ChemAxon
Polar Surface Area337.86 ŲChemAxon
Rotatable Bond Count11ChemAxon
Refractivity244.79 m³·mol⁻¹ChemAxon
Polarizability110.87 ųChemAxon
Number of Rings10ChemAxon
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-2H]-345.25230932474
DeepCCS[M+Na]+319.2730932474
AllCCS[M+H]+298.332859911
AllCCS[M+H-H2O]+298.932859911
AllCCS[M+NH4]+297.732859911
AllCCS[M+Na]+297.532859911
AllCCS[M-H]-281.932859911
AllCCS[M+Na-2H]-288.232859911
AllCCS[M+HCOO]-294.932859911

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Experimental LC-MS/MSLC-MS/MS Spectrum - Tomatine 6V, Positive-QTOFsplash10-001i-9000000000-2d0e0cccacc5de1c1d982021-09-20HMDB team, MONAView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tomatine 10V, Positive-QTOFsplash10-0gb9-5204670292-fefb24de6d82cf624d9e2015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tomatine 20V, Positive-QTOFsplash10-014i-0214950550-746c6066dceba3c1c1f42015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tomatine 40V, Positive-QTOFsplash10-014r-2307930620-f9c49ce8d08133042e042015-04-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tomatine 10V, Negative-QTOFsplash10-03fr-9602540041-49730afc04a87b1ba5562015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tomatine 20V, Negative-QTOFsplash10-03fr-5901730121-29848bddc6af802971d02015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tomatine 40V, Negative-QTOFsplash10-03fr-4902610100-a4eb02a2dcccce405c802015-04-25Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tomatine 10V, Positive-QTOFsplash10-001i-9000200010-0880a3964aaaa89784552021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tomatine 20V, Positive-QTOFsplash10-00ls-6309310021-87a1da82a62eb8f896242021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tomatine 40V, Positive-QTOFsplash10-0a6r-5232900013-40916e3761a4a30c788b2021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tomatine 10V, Negative-QTOFsplash10-001i-9000010001-553f7d4162d435d3da112021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tomatine 20V, Negative-QTOFsplash10-0a59-9100000028-2c472296ac894f5854a72021-09-22Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tomatine 40V, Negative-QTOFsplash10-052f-9002210314-69b0c89546960ad0f26d2021-09-22Wishart LabView Spectrum

NMR Spectra

Spectrum TypeDescriptionDeposition DateSourceView
Predicted 1D NMR1H NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 100 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 1000 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 200 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 300 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 400 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 500 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 600 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 700 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 800 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR1H NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Predicted 1D NMR13C NMR Spectrum (1D, 900 MHz, D2O, predicted)2021-09-25Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Cytoplasm
  • 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 IDFDB012367
KNApSAcK IDC00002268
Chemspider ID5312
KEGG Compound IDC10827
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkTomatine
METLIN IDNot Available
PubChem Compound5513
PDB IDNot Available
ChEBI ID9630
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 References
  1. Friedman M, Levin CE, Lee SU, Kim HJ, Lee IS, Byun JO, Kozukue N: Tomatine-containing green tomato extracts inhibit growth of human breast, colon, liver, and stomach cancer cells. J Agric Food Chem. 2009 Jul 8;57(13):5727-33. doi: 10.1021/jf900364j. [PubMed:19514731 ]
  2. Seipke RF, Loria R: Streptomyces scabies 87-22 possesses a functional tomatinase. J Bacteriol. 2008 Dec;190(23):7684-92. doi: 10.1128/JB.01010-08. Epub 2008 Oct 3. [PubMed:18835993 ]
  3. Cayen MN: Effect of dietary tomatine on cholesterol metabolism in the rat. J Lipid Res. 1971 Jul;12(4):482-90. [PubMed:4362143 ]
  4. Friedman M, Fitch TE, Yokoyama WE: Lowering of plasma LDL cholesterol in hamsters by the tomato glycoalkaloid tomatine. Food Chem Toxicol. 2000 Jul;38(7):549-53. [PubMed:10942315 ]
  5. Morrow WJ, Yang YW, Sheikh NA: Immunobiology of the Tomatine adjuvant. Vaccine. 2004 Jun 23;22(19):2380-4. [PubMed:15193398 ]
  6. Simons K, Toomre D: Lipid rafts and signal transduction. Nat Rev Mol Cell Biol. 2000 Oct;1(1):31-9. [PubMed:11413487 ]
  7. 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 ]
  8. 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 ]
  9. 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 ]
  10. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
  11. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.