Hmdb loader

Showing metabocard for Vinaginsenoside R7 (HMDB0040805)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 02:23:26 UTC
Update Date2022-03-07 02:56:44 UTC
HMDB IDHMDB0040805
Secondary Accession Numbers
  • HMDB40805
Metabolite Identification
Common NameVinaginsenoside R7
DescriptionVinaginsenoside R7 belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units. Based on a literature review a significant number of articles have been published on Vinaginsenoside R7.
Structure
Data?1563863589
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0040805 (Vinaginsenoside R7)


  Mrv0541 02241209182D          

 75 82  0  0  0  0            999 V2000
    5.1474    4.4864    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.8928    2.6995    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.2436    0.1396    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8309    0.8548    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0040805 (Vinaginsenoside R7)

HMDB0040805
     RDKit          3D
Vinaginsenoside R7
165172  0  0  0  0  0  0  0  0999 V2000
   -8.2013    5.6389   -1.9733 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9524    4.1988   -1.5771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1156    3.9100   -0.1430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6075    3.2996   -2.4523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3064    1.8912   -2.4129 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4341    1.1146   -1.1655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0358   -0.3480   -1.3371 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9935   -0.8665   -2.4225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2227   -0.9254   -0.1399 O   0  0  0  0  0  0  0  0  0  0  0  0
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  -10.7205   -3.3161   -0.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
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   10.1706    0.4512    1.5974 O   0  0  0  0  0  0  0  0  0  0  0  0
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    9.3731   -0.4076   -4.0042 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7539    0.0107   -4.4125 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3712   -1.0273   -5.1498 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5874    0.1935   -3.1697 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7971    0.8328   -3.4452 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8608    1.0639   -2.1393 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6708    1.0916   -1.0140 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2298   -0.3595    1.0208 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0040805 (Vinaginsenoside R7)


  Mrv0541 02241209182D          

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M  END
> <DATABASE_ID>
HMDB0040805

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)=CCCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4OC4OCC(O)C(O)C4O)C(C)(C)C3CCC21C

> <INCHI_IDENTIFIER>
InChI=1S/C53H90O22/c1-23(2)10-9-14-53(8,75-46-42(67)38(63)35(60)27(19-54)69-46)24-11-16-52(7)33(24)25(57)18-31-50(5)15-13-32(49(3,4)30(50)12-17-51(31,52)6)72-47-43(39(64)36(61)28(20-55)70-47)74-48-44(40(65)37(62)29(21-56)71-48)73-45-41(66)34(59)26(58)22-68-45/h10,24-48,54-67H,9,11-22H2,1-8H3

> <INCHI_KEY>
ZXPNUZXGLAHYEE-UHFFFAOYSA-N

> <FORMULA>
C53H90O22

> <MOLECULAR_WEIGHT>
1079.2685

> <EXACT_MASS>
1078.592374564

> <JCHEM_ACCEPTOR_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
115.79359176939973

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
14

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
2-[(2-{5-[(3-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-16-hydroxy-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl}-6-methylhept-5-en-2-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <ALOGPS_LOGP>
-0.07

> <JCHEM_LOGP>
-0.9210698356666672

> <ALOGPS_LOGS>
-3.04

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
8

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.29109973778368

> <JCHEM_PKA_STRONGEST_ACIDIC>
11.842808630151657

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6486743728420787

> <JCHEM_POLAR_SURFACE_AREA>
357.06000000000006

> <JCHEM_REFRACTIVITY>
260.92660000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
15

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.85e-01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-[(2-{5-[(3-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-16-hydroxy-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl}-6-methylhept-5-en-2-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0040805 (Vinaginsenoside R7)

HMDB0040805
     RDKit          3D
Vinaginsenoside R7
165172  0  0  0  0  0  0  0  0999 V2000
   -8.2013    5.6389   -1.9733 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9524    4.1988   -1.5771 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1156    3.9100   -0.1430 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6075    3.2996   -2.4523 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3064    1.8912   -2.4129 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4341    1.1146   -1.1655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0358   -0.3480   -1.3371 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9935   -0.8665   -2.4225 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2227   -0.9254   -0.1399 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3853   -1.0359    0.4992 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6625   -2.4443    0.4154 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8765   -2.7720    0.9418 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7205   -3.3161   -0.2203 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1462   -4.4321   -0.8045 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6611   -1.6588    1.5430 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6618   -2.2641    2.3425 O   0  0  0  0  0  0  0  0  0  0  0  0
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  -10.3190    0.5350    2.2731 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4077   -0.7785    1.9680 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7568   -1.8320    2.6280 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6591   -0.6200   -1.8361 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6134   -2.1640   -1.8531 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3158   -2.5710   -1.2096 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5046   -1.3610   -1.4715 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.4863   -0.2276   -1.0770 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7721    1.0374   -1.3663 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3182    2.1518   -0.6725 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3278    1.1501   -0.9898 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5252   -0.0840   -1.2655 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0693    0.0317   -1.1539 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4054   -0.2577   -2.6231 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4400    1.4343   -0.9373 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9201    1.3548   -0.6662 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1547    0.8053    0.7238 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4415    0.4144    0.9487 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2147    1.1749    1.7575 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7635    0.4971    2.8678 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6504    1.3257    3.5229 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1214    1.4409    4.9611 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1036    0.1644    5.4859 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7555    2.7171    3.0138 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.7264    3.5652    3.4898 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.9361    2.8426    1.5175 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2050    3.9012    0.9982 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4703    1.5385    0.9248 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4467    0.6025    1.1532 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.8657   -0.1561    0.1023 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7084   -1.4927    0.4915 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.2392   -1.8069    1.7042 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.4656   -3.3246    1.7676 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0170   -3.6698    3.0219 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4147   -1.0596    2.1931 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.5079   -1.9641    2.1645 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.8509    0.1383    1.4111 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.1706    0.4512    1.5974 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.4007   -0.0074    0.0013 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.7788    0.9577   -0.8840 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.5140    0.4645   -1.9364 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.8333    0.5695   -3.1575 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.3731   -0.4076   -4.0042 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7539    0.0107   -4.4125 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3712   -1.0273   -5.1498 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.5874    0.1935   -3.1697 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7971    0.8328   -3.4452 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.8608    1.0639   -2.1393 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6708    1.0916   -1.0140 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2298   -0.3595    1.0208 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9923   -1.4474    1.7869 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2455    0.1170    2.0410 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5811   -0.8926   -0.2238 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1017   -2.1690    0.0336 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4067   -2.4359   -0.6882 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2466   -1.2228   -0.6471 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6802   -1.0281    0.7892 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3433    6.2785   -1.7800 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5339    5.6150   -3.0277 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1062    5.9902   -1.3917 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5889    4.8027    0.3643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.7615    3.0763    0.1213 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1370    3.7732    0.3721 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5248    3.7415   -3.5066 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2111    1.7963   -2.7211 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7970    1.3301   -3.2922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5496    1.0388   -0.9567 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0259    1.5441   -0.2616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1384   -1.9553   -2.3869 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9582   -0.3755   -2.4131 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.5526   -0.6718   -3.4440 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2932   -0.6090    0.0128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8277   -3.6032    1.6837 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.6262   -4.9758   -0.1891 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2514   -1.0803    0.7825 H   0  0  0  0  0  0  0  0  0  0  0  0
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    0.3752    2.0471   -1.8710 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0342    2.0150   -0.1641 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4532    0.8622   -1.4675 H   0  0  0  0  0  0  0  0  0  0  0  0
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    3.6802    2.0679    2.0592 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6722    0.8679    3.6488 H   0  0  0  0  0  0  0  0  0  0  0  0
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    5.8612    2.0249    5.5640 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6691    0.0540    6.2869 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.6939    3.1520    3.4701 H   0  0  0  0  0  0  0  0  0  0  0  0
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    7.0120    3.0212    1.2421 H   0  0  0  0  0  0  0  0  0  0  0  0
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    6.3953   -0.0003   -0.8611 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4090   -1.6343    2.4583 H   0  0  0  0  0  0  0  0  0  0  0  0
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   10.2772   -1.4054    2.5051 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2631    1.0095    1.8375 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2744    1.4473    1.5440 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8241   -0.9816   -0.3830 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6402   -0.6432   -1.7904 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4828   -1.3305   -3.3666 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.7040   -0.5988   -4.8760 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7615    0.9477   -4.9905 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4883   -1.8084   -4.5363 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.8120   -0.7740   -2.6867 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.4830    0.2002   -3.7976 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.7730    2.0803   -2.5774 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.1373    1.9629   -0.9046 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.4427   -0.9101    2.6503 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6974   -1.9896    1.1594 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3247   -2.1996    2.2452 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8224    0.8141    2.7276 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0783   -0.6895    2.7414 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5819    0.7257    1.6821 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.5456   -1.2382   -0.8289 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3008   -2.3798    1.1176 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5145   -3.0856   -0.2646 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2040   -2.8448   -1.6934 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9179   -3.2522   -0.1357 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9812   -1.5002    1.5074 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6507   -1.5520    1.0195 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8297   -0.0027    1.1029 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0040805 (Vinaginsenoside R7)

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0       9.608   8.375   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.185   6.893   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       7.688   6.518   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       7.267   5.039   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.746   4.613   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       6.055   0.261   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.284   1.596   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.761   1.218   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       7.647   2.320   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       6.769   3.557   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.148   3.152   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       3.941   3.879   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       2.637   3.154   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       2.609   1.637   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       3.918   0.841   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0       5.235   0.050   0.000  0.00  0.00           C+0
HETATM   17  O   UNK     0       3.970   5.465   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0       3.895  -0.695   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.542  -1.444   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       1.220  -0.651   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       1.253   0.885   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.279   2.430   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      12.174   7.638   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.103   8.744   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      11.529  10.226   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      -0.072   1.681   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      -1.420   0.936   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -1.446  -0.605   0.000  0.00  0.00           C+0
HETATM   29  O   UNK     0      -2.793  -1.352   0.000  0.00  0.00           O+0
HETATM   30  C   UNK     0      -4.116  -0.559   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -4.088   0.982   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -5.408   1.775   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -5.379   3.319   0.000  0.00  0.00           C+0
HETATM   34  O   UNK     0      -6.702   4.112   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      -8.158  -2.800   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0      -9.503  -3.545   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -10.826  -2.751   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0     -12.174  -3.501   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      -1.135  -2.559   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -0.126  -1.398   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       0.845  -2.595   0.000  0.00  0.00           C+0
HETATM   42  O   UNK     0       5.785   5.465   0.000  0.00  0.00           O+0
HETATM   43  C   UNK     0       5.413   6.957   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0       6.519   8.026   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0       6.150   9.525   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       7.256  10.593   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0       6.881  12.088   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0       2.822   6.313   0.000  0.00  0.00           O+0
HETATM   49  C   UNK     0       3.931   7.384   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0       3.559   8.878   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0       4.666   9.946   0.000  0.00  0.00           C+0
HETATM   52  O   UNK     0       4.293  11.443   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0       2.077   9.302   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      -8.078   1.822   0.000  0.00  0.00           O+0
HETATM   55  C   UNK     0      -6.756   1.028   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -6.781  -0.510   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      -5.461  -1.303   0.000  0.00  0.00           C+0
HETATM   58  O   UNK     0      -5.490  -2.844   0.000  0.00  0.00           O+0
HETATM   59  C   UNK     0      -6.838  -3.593   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      -6.864  -5.132   0.000  0.00  0.00           C+0
HETATM   61  O   UNK     0      -5.541  -5.925   0.000  0.00  0.00           O+0
HETATM   62  C   UNK     0      -5.569  -7.468   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0      -4.250  -8.262   0.000  0.00  0.00           C+0
HETATM   64  O   UNK     0      -2.902  -7.512   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0      -8.130  -1.257   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0      -2.953 -10.591   0.000  0.00  0.00           O+0
HETATM   67  C   UNK     0      -4.275  -9.797   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      -5.623 -10.547   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0      -6.943  -9.754   0.000  0.00  0.00           C+0
HETATM   70  O   UNK     0      -6.915  -8.210   0.000  0.00  0.00           O+0
HETATM   71  O   UNK     0     -10.877  -5.830   0.000  0.00  0.00           O+0
HETATM   72  C   UNK     0      -9.531  -5.088   0.000  0.00  0.00           C+0
HETATM   73  C   UNK     0      -8.211  -5.881   0.000  0.00  0.00           C+0
HETATM   74  O   UNK     0      -8.237  -7.417   0.000  0.00  0.00           O+0
HETATM   75  O   UNK     0      -5.652 -12.088   0.000  0.00  0.00           O+0
CONECT    1    2   24                                                       
CONECT    2    1    3                                                       
CONECT    3    2    4                                                       
CONECT    4    3    5   10   42                                             
CONECT    5    4                                                            
CONECT    6    7                                                            
CONECT    7    6    8   11   15                                             
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    4    9   11                                                  
CONECT   11    7   10   12                                                  
CONECT   12   11   13   17                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15   21                                                  
CONECT   15    7   14   16   18                                             
CONECT   16   15                                                            
CONECT   17   12                                                            
CONECT   18   15   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   40                                                  
CONECT   21   14   20   22   26                                             
CONECT   22   21                                                            
CONECT   23   24                                                            
CONECT   24    1   23   25                                                  
CONECT   25   24                                                            
CONECT   26   21   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29   40                                                  
CONECT   29   28   30                                                       
CONECT   30   29   31   57                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33   55                                                  
CONECT   33   32   34                                                       
CONECT   34   33                                                            
CONECT   35   36   59                                                       
CONECT   36   35   37   72                                                  
CONECT   37   36   38                                                       
CONECT   38   37                                                            
CONECT   39   40                                                            
CONECT   40   20   28   39   41                                             
CONECT   41   40                                                            
CONECT   42    4   43                                                       
CONECT   43   42   44   49                                                  
CONECT   44   43   45                                                       
CONECT   45   44   46   51                                                  
CONECT   46   45   47                                                       
CONECT   47   46                                                            
CONECT   48   49                                                            
CONECT   49   43   48   50                                                  
CONECT   50   49   51   53                                                  
CONECT   51   45   50   52                                                  
CONECT   52   51                                                            
CONECT   53   50                                                            
CONECT   54   55                                                            
CONECT   55   32   54   56                                                  
CONECT   56   55   57   65                                                  
CONECT   57   30   56   58                                                  
CONECT   58   57   59                                                       
CONECT   59   35   58   60                                                  
CONECT   60   59   61   73                                                  
CONECT   61   60   62                                                       
CONECT   62   61   63   70                                                  
CONECT   63   62   64   67                                                  
CONECT   64   63                                                            
CONECT   65   56                                                            
CONECT   66   67                                                            
CONECT   67   63   66   68                                                  
CONECT   68   67   69   75                                                  
CONECT   69   68   70                                                       
CONECT   70   62   69                                                       
CONECT   71   72                                                            
CONECT   72   36   71   73                                                  
CONECT   73   60   72   74                                                  
CONECT   74   73                                                            
CONECT   75   68                                                            
MASTER        0    0    0    0    0    0    0    0   75    0  164    0
END
Download

3D PDB for HMDB0040805 (Vinaginsenoside R7)

COMPND    HMDB0040805
HETATM    1  C1  UNL     1      -8.201   5.639  -1.973  1.00  0.00           C  
HETATM    2  C2  UNL     1      -7.952   4.199  -1.577  1.00  0.00           C  
HETATM    3  C3  UNL     1      -8.116   3.910  -0.143  1.00  0.00           C  
HETATM    4  C4  UNL     1      -7.607   3.300  -2.452  1.00  0.00           C  
HETATM    5  C5  UNL     1      -7.306   1.891  -2.413  1.00  0.00           C  
HETATM    6  C6  UNL     1      -7.434   1.115  -1.166  1.00  0.00           C  
HETATM    7  C7  UNL     1      -7.036  -0.348  -1.337  1.00  0.00           C  
HETATM    8  C8  UNL     1      -7.994  -0.867  -2.422  1.00  0.00           C  
HETATM    9  O1  UNL     1      -7.223  -0.925  -0.140  1.00  0.00           O  
HETATM   10  C9  UNL     1      -8.385  -1.036   0.499  1.00  0.00           C  
HETATM   11  O2  UNL     1      -8.662  -2.444   0.415  1.00  0.00           O  
HETATM   12  C10 UNL     1      -9.877  -2.772   0.942  1.00  0.00           C  
HETATM   13  C11 UNL     1     -10.721  -3.316  -0.220  1.00  0.00           C  
HETATM   14  O3  UNL     1     -10.146  -4.432  -0.804  1.00  0.00           O  
HETATM   15  C12 UNL     1     -10.661  -1.659   1.543  1.00  0.00           C  
HETATM   16  O4  UNL     1     -11.662  -2.264   2.343  1.00  0.00           O  
HETATM   17  C13 UNL     1      -9.845  -0.790   2.436  1.00  0.00           C  
HETATM   18  O5  UNL     1     -10.319   0.535   2.273  1.00  0.00           O  
HETATM   19  C14 UNL     1      -8.408  -0.779   1.968  1.00  0.00           C  
HETATM   20  O6  UNL     1      -7.757  -1.832   2.628  1.00  0.00           O  
HETATM   21  C15 UNL     1      -5.659  -0.620  -1.836  1.00  0.00           C  
HETATM   22  C16 UNL     1      -5.613  -2.164  -1.853  1.00  0.00           C  
HETATM   23  C17 UNL     1      -4.316  -2.571  -1.210  1.00  0.00           C  
HETATM   24  C18 UNL     1      -3.505  -1.361  -1.471  1.00  0.00           C  
HETATM   25  C19 UNL     1      -3.288  -1.338  -2.956  1.00  0.00           C  
HETATM   26  C20 UNL     1      -4.486  -0.228  -1.077  1.00  0.00           C  
HETATM   27  C21 UNL     1      -3.772   1.037  -1.366  1.00  0.00           C  
HETATM   28  O7  UNL     1      -4.318   2.152  -0.672  1.00  0.00           O  
HETATM   29  C22 UNL     1      -2.328   1.150  -0.990  1.00  0.00           C  
HETATM   30  C23 UNL     1      -1.525  -0.084  -1.265  1.00  0.00           C  
HETATM   31  C24 UNL     1      -0.069   0.032  -1.154  1.00  0.00           C  
HETATM   32  C25 UNL     1       0.405  -0.258  -2.623  1.00  0.00           C  
HETATM   33  C26 UNL     1       0.440   1.434  -0.937  1.00  0.00           C  
HETATM   34  C27 UNL     1       1.920   1.355  -0.666  1.00  0.00           C  
HETATM   35  C28 UNL     1       2.155   0.805   0.724  1.00  0.00           C  
HETATM   36  O8  UNL     1       3.441   0.414   0.949  1.00  0.00           O  
HETATM   37  C29 UNL     1       4.215   1.175   1.758  1.00  0.00           C  
HETATM   38  O9  UNL     1       4.763   0.497   2.868  1.00  0.00           O  
HETATM   39  C30 UNL     1       5.650   1.326   3.523  1.00  0.00           C  
HETATM   40  C31 UNL     1       5.121   1.441   4.961  1.00  0.00           C  
HETATM   41  O10 UNL     1       5.104   0.164   5.486  1.00  0.00           O  
HETATM   42  C32 UNL     1       5.755   2.717   3.014  1.00  0.00           C  
HETATM   43  O11 UNL     1       4.726   3.565   3.490  1.00  0.00           O  
HETATM   44  C33 UNL     1       5.936   2.843   1.517  1.00  0.00           C  
HETATM   45  O12 UNL     1       5.205   3.901   0.998  1.00  0.00           O  
HETATM   46  C34 UNL     1       5.470   1.539   0.925  1.00  0.00           C  
HETATM   47  O13 UNL     1       6.447   0.602   1.153  1.00  0.00           O  
HETATM   48  C35 UNL     1       6.866  -0.156   0.102  1.00  0.00           C  
HETATM   49  O14 UNL     1       6.708  -1.493   0.491  1.00  0.00           O  
HETATM   50  C36 UNL     1       7.239  -1.807   1.704  1.00  0.00           C  
HETATM   51  C37 UNL     1       7.466  -3.325   1.768  1.00  0.00           C  
HETATM   52  O15 UNL     1       8.017  -3.670   3.022  1.00  0.00           O  
HETATM   53  C38 UNL     1       8.415  -1.060   2.193  1.00  0.00           C  
HETATM   54  O16 UNL     1       9.508  -1.964   2.164  1.00  0.00           O  
HETATM   55  C39 UNL     1       8.851   0.138   1.411  1.00  0.00           C  
HETATM   56  O17 UNL     1      10.171   0.451   1.597  1.00  0.00           O  
HETATM   57  C40 UNL     1       8.401  -0.007   0.001  1.00  0.00           C  
HETATM   58  O18 UNL     1       8.779   0.958  -0.884  1.00  0.00           O  
HETATM   59  C41 UNL     1       9.514   0.464  -1.936  1.00  0.00           C  
HETATM   60  O19 UNL     1       8.833   0.569  -3.157  1.00  0.00           O  
HETATM   61  C42 UNL     1       9.373  -0.408  -4.004  1.00  0.00           C  
HETATM   62  C43 UNL     1      10.754   0.011  -4.413  1.00  0.00           C  
HETATM   63  O20 UNL     1      11.371  -1.027  -5.150  1.00  0.00           O  
HETATM   64  C44 UNL     1      11.587   0.193  -3.170  1.00  0.00           C  
HETATM   65  O21 UNL     1      12.797   0.833  -3.445  1.00  0.00           O  
HETATM   66  C45 UNL     1      10.861   1.064  -2.139  1.00  0.00           C  
HETATM   67  O22 UNL     1      11.671   1.092  -1.014  1.00  0.00           O  
HETATM   68  C46 UNL     1       1.230  -0.360   1.021  1.00  0.00           C  
HETATM   69  C47 UNL     1       1.992  -1.447   1.787  1.00  0.00           C  
HETATM   70  C48 UNL     1       0.245   0.117   2.041  1.00  0.00           C  
HETATM   71  C49 UNL     1       0.581  -0.893  -0.224  1.00  0.00           C  
HETATM   72  C50 UNL     1      -0.102  -2.169   0.034  1.00  0.00           C  
HETATM   73  C51 UNL     1      -1.407  -2.436  -0.688  1.00  0.00           C  
HETATM   74  C52 UNL     1      -2.247  -1.223  -0.647  1.00  0.00           C  
HETATM   75  C53 UNL     1      -2.680  -1.028   0.789  1.00  0.00           C  
HETATM   76  H1  UNL     1      -7.343   6.279  -1.780  1.00  0.00           H  
HETATM   77  H2  UNL     1      -8.534   5.615  -3.028  1.00  0.00           H  
HETATM   78  H3  UNL     1      -9.106   5.990  -1.392  1.00  0.00           H  
HETATM   79  H4  UNL     1      -8.589   4.803   0.364  1.00  0.00           H  
HETATM   80  H5  UNL     1      -8.762   3.076   0.121  1.00  0.00           H  
HETATM   81  H6  UNL     1      -7.137   3.773   0.372  1.00  0.00           H  
HETATM   82  H7  UNL     1      -7.525   3.742  -3.507  1.00  0.00           H  
HETATM   83  H8  UNL     1      -6.211   1.796  -2.721  1.00  0.00           H  
HETATM   84  H9  UNL     1      -7.797   1.330  -3.292  1.00  0.00           H  
HETATM   85  H10 UNL     1      -8.550   1.039  -0.957  1.00  0.00           H  
HETATM   86  H11 UNL     1      -7.026   1.544  -0.262  1.00  0.00           H  
HETATM   87  H12 UNL     1      -8.138  -1.955  -2.387  1.00  0.00           H  
HETATM   88  H13 UNL     1      -8.958  -0.375  -2.413  1.00  0.00           H  
HETATM   89  H14 UNL     1      -7.553  -0.672  -3.444  1.00  0.00           H  
HETATM   90  H15 UNL     1      -9.293  -0.609   0.013  1.00  0.00           H  
HETATM   91  H16 UNL     1      -9.828  -3.603   1.684  1.00  0.00           H  
HETATM   92  H17 UNL     1     -10.867  -2.524  -0.981  1.00  0.00           H  
HETATM   93  H18 UNL     1     -11.737  -3.597   0.128  1.00  0.00           H  
HETATM   94  H19 UNL     1      -9.626  -4.976  -0.189  1.00  0.00           H  
HETATM   95  H20 UNL     1     -11.251  -1.080   0.783  1.00  0.00           H  
HETATM   96  H21 UNL     1     -12.404  -2.581   1.764  1.00  0.00           H  
HETATM   97  H22 UNL     1      -9.938  -1.062   3.509  1.00  0.00           H  
HETATM   98  H23 UNL     1     -10.942   0.769   3.009  1.00  0.00           H  
HETATM   99  H24 UNL     1      -7.954   0.144   2.302  1.00  0.00           H  
HETATM  100  H25 UNL     1      -8.285  -2.176   3.393  1.00  0.00           H  
HETATM  101  H26 UNL     1      -5.549  -0.242  -2.878  1.00  0.00           H  
HETATM  102  H27 UNL     1      -5.823  -2.588  -2.830  1.00  0.00           H  
HETATM  103  H28 UNL     1      -6.390  -2.601  -1.174  1.00  0.00           H  
HETATM  104  H29 UNL     1      -4.401  -2.928  -0.193  1.00  0.00           H  
HETATM  105  H30 UNL     1      -3.865  -3.422  -1.798  1.00  0.00           H  
HETATM  106  H31 UNL     1      -4.069  -1.966  -3.501  1.00  0.00           H  
HETATM  107  H32 UNL     1      -3.370  -0.359  -3.441  1.00  0.00           H  
HETATM  108  H33 UNL     1      -2.357  -1.823  -3.302  1.00  0.00           H  
HETATM  109  H34 UNL     1      -4.733  -0.273   0.006  1.00  0.00           H  
HETATM  110  H35 UNL     1      -3.906   1.306  -2.435  1.00  0.00           H  
HETATM  111  H36 UNL     1      -4.645   1.835   0.209  1.00  0.00           H  
HETATM  112  H37 UNL     1      -1.897   1.956  -1.659  1.00  0.00           H  
HETATM  113  H38 UNL     1      -2.132   1.499   0.026  1.00  0.00           H  
HETATM  114  H39 UNL     1      -1.717  -0.206  -2.399  1.00  0.00           H  
HETATM  115  H40 UNL     1      -0.086  -1.177  -2.998  1.00  0.00           H  
HETATM  116  H41 UNL     1       0.115   0.654  -3.178  1.00  0.00           H  
HETATM  117  H42 UNL     1       1.465  -0.399  -2.696  1.00  0.00           H  
HETATM  118  H43 UNL     1       0.375   2.047  -1.871  1.00  0.00           H  
HETATM  119  H44 UNL     1      -0.034   2.015  -0.164  1.00  0.00           H  
HETATM  120  H45 UNL     1       2.453   0.862  -1.467  1.00  0.00           H  
HETATM  121  H46 UNL     1       2.290   2.424  -0.689  1.00  0.00           H  
HETATM  122  H47 UNL     1       1.959   1.677   1.371  1.00  0.00           H  
HETATM  123  H48 UNL     1       3.680   2.068   2.059  1.00  0.00           H  
HETATM  124  H49 UNL     1       6.672   0.868   3.649  1.00  0.00           H  
HETATM  125  H50 UNL     1       4.154   1.972   4.997  1.00  0.00           H  
HETATM  126  H51 UNL     1       5.861   2.025   5.564  1.00  0.00           H  
HETATM  127  H52 UNL     1       5.669   0.054   6.287  1.00  0.00           H  
HETATM  128  H53 UNL     1       6.694   3.152   3.470  1.00  0.00           H  
HETATM  129  H54 UNL     1       4.918   4.498   3.315  1.00  0.00           H  
HETATM  130  H55 UNL     1       7.012   3.021   1.242  1.00  0.00           H  
HETATM  131  H56 UNL     1       5.131   3.836   0.016  1.00  0.00           H  
HETATM  132  H57 UNL     1       5.182   1.598  -0.139  1.00  0.00           H  
HETATM  133  H58 UNL     1       6.395  -0.000  -0.861  1.00  0.00           H  
HETATM  134  H59 UNL     1       6.409  -1.634   2.458  1.00  0.00           H  
HETATM  135  H60 UNL     1       8.094  -3.684   0.930  1.00  0.00           H  
HETATM  136  H61 UNL     1       6.512  -3.887   1.716  1.00  0.00           H  
HETATM  137  H62 UNL     1       8.879  -4.110   2.897  1.00  0.00           H  
HETATM  138  H63 UNL     1       8.326  -0.827   3.298  1.00  0.00           H  
HETATM  139  H64 UNL     1      10.277  -1.405   2.505  1.00  0.00           H  
HETATM  140  H65 UNL     1       8.263   1.009   1.838  1.00  0.00           H  
HETATM  141  H66 UNL     1      10.274   1.447   1.544  1.00  0.00           H  
HETATM  142  H67 UNL     1       8.824  -0.982  -0.383  1.00  0.00           H  
HETATM  143  H68 UNL     1       9.640  -0.643  -1.790  1.00  0.00           H  
HETATM  144  H69 UNL     1       9.483  -1.330  -3.367  1.00  0.00           H  
HETATM  145  H70 UNL     1       8.704  -0.599  -4.876  1.00  0.00           H  
HETATM  146  H71 UNL     1      10.762   0.948  -4.991  1.00  0.00           H  
HETATM  147  H72 UNL     1      11.488  -1.808  -4.536  1.00  0.00           H  
HETATM  148  H73 UNL     1      11.812  -0.774  -2.687  1.00  0.00           H  
HETATM  149  H74 UNL     1      13.483   0.200  -3.798  1.00  0.00           H  
HETATM  150  H75 UNL     1      10.773   2.080  -2.577  1.00  0.00           H  
HETATM  151  H76 UNL     1      12.137   1.963  -0.905  1.00  0.00           H  
HETATM  152  H77 UNL     1       2.443  -0.910   2.650  1.00  0.00           H  
HETATM  153  H78 UNL     1       2.697  -1.990   1.159  1.00  0.00           H  
HETATM  154  H79 UNL     1       1.325  -2.200   2.245  1.00  0.00           H  
HETATM  155  H80 UNL     1       0.822   0.814   2.728  1.00  0.00           H  
HETATM  156  H81 UNL     1      -0.078  -0.690   2.741  1.00  0.00           H  
HETATM  157  H82 UNL     1      -0.582   0.726   1.682  1.00  0.00           H  
HETATM  158  H83 UNL     1       1.546  -1.238  -0.829  1.00  0.00           H  
HETATM  159  H84 UNL     1      -0.301  -2.380   1.118  1.00  0.00           H  
HETATM  160  H85 UNL     1       0.514  -3.086  -0.265  1.00  0.00           H  
HETATM  161  H86 UNL     1      -1.204  -2.845  -1.693  1.00  0.00           H  
HETATM  162  H87 UNL     1      -1.918  -3.252  -0.136  1.00  0.00           H  
HETATM  163  H88 UNL     1      -1.981  -1.500   1.507  1.00  0.00           H  
HETATM  164  H89 UNL     1      -3.651  -1.552   1.019  1.00  0.00           H  
HETATM  165  H90 UNL     1      -2.830  -0.003   1.103  1.00  0.00           H  
CONECT    1    2   76   77   78
CONECT    2    3    4    4
CONECT    3   79   80   81
CONECT    4    5   82
CONECT    5    6   83   84
CONECT    6    7   85   86
CONECT    7    8    9   21
CONECT    8   87   88   89
CONECT    9   10
CONECT   10   11   19   90
CONECT   11   12
CONECT   12   13   15   91
CONECT   13   14   92   93
CONECT   14   94
CONECT   15   16   17   95
CONECT   16   96
CONECT   17   18   19   97
CONECT   18   98
CONECT   19   20   99
CONECT   20  100
CONECT   21   22   26  101
CONECT   22   23  102  103
CONECT   23   24  104  105
CONECT   24   25   26   74
CONECT   25  106  107  108
CONECT   26   27  109
CONECT   27   28   29  110
CONECT   28  111
CONECT   29   30  112  113
CONECT   30   31   74  114
CONECT   31   32   33   71
CONECT   32  115  116  117
CONECT   33   34  118  119
CONECT   34   35  120  121
CONECT   35   36   68  122
CONECT   36   37
CONECT   37   38   46  123
CONECT   38   39
CONECT   39   40   42  124
CONECT   40   41  125  126
CONECT   41  127
CONECT   42   43   44  128
CONECT   43  129
CONECT   44   45   46  130
CONECT   45  131
CONECT   46   47  132
CONECT   47   48
CONECT   48   49   57  133
CONECT   49   50
CONECT   50   51   53  134
CONECT   51   52  135  136
CONECT   52  137
CONECT   53   54   55  138
CONECT   54  139
CONECT   55   56   57  140
CONECT   56  141
CONECT   57   58  142
CONECT   58   59
CONECT   59   60   66  143
CONECT   60   61
CONECT   61   62  144  145
CONECT   62   63   64  146
CONECT   63  147
CONECT   64   65   66  148
CONECT   65  149
CONECT   66   67  150
CONECT   67  151
CONECT   68   69   70   71
CONECT   69  152  153  154
CONECT   70  155  156  157
CONECT   71   72  158
CONECT   72   73  159  160
CONECT   73   74  161  162
CONECT   74   75
CONECT   75  163  164  165
END
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SMILES for HMDB0040805 (Vinaginsenoside R7)

CC(C)=CCCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4OC4OCC(O)C(O)C4O)C(C)(C)C3CCC21C
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INCHI for HMDB0040805 (Vinaginsenoside R7)

InChI=1S/C53H90O22/c1-23(2)10-9-14-53(8,75-46-42(67)38(63)35(60)27(19-54)69-46)24-11-16-52(7)33(24)25(57)18-31-50(5)15-13-32(49(3,4)30(50)12-17-51(31,52)6)72-47-43(39(64)36(61)28(20-55)70-47)74-48-44(40(65)37(62)29(21-56)71-48)73-45-41(66)34(59)26(58)22-68-45/h10,24-48,54-67H,9,11-22H2,1-8H3
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View in JSmolView NMR AssignmentsView Stereo Labels
SynonymsNot Available
Chemical FormulaC53H90O22
Average Molecular Weight1079.2685
Monoisotopic Molecular Weight1078.592374564
IUPAC Name2-[(2-{5-[(3-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-16-hydroxy-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl}-6-methylhept-5-en-2-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol
Traditional Name2-[(2-{5-[(3-{[4,5-dihydroxy-6-(hydroxymethyl)-3-[(3,4,5-trihydroxyoxan-2-yl)oxy]oxan-2-yl]oxy}-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl)oxy]-16-hydroxy-2,6,6,10,11-pentamethyltetracyclo[8.7.0.0²,⁷.0¹¹,¹⁵]heptadecan-14-yl}-6-methylhept-5-en-2-yl)oxy]-6-(hydroxymethyl)oxane-3,4,5-triol
CAS Registry Number156009-83-5
SMILES
CC(C)=CCCC(C)(OC1OC(CO)C(O)C(O)C1O)C1CCC2(C)C1C(O)CC1C3(C)CCC(OC4OC(CO)C(O)C(O)C4OC4OC(CO)C(O)C(O)C4OC4OCC(O)C(O)C4O)C(C)(C)C3CCC21C
InChI Identifier
InChI=1S/C53H90O22/c1-23(2)10-9-14-53(8,75-46-42(67)38(63)35(60)27(19-54)69-46)24-11-16-52(7)33(24)25(57)18-31-50(5)15-13-32(49(3,4)30(50)12-17-51(31,52)6)72-47-43(39(64)36(61)28(20-55)70-47)74-48-44(40(65)37(62)29(21-56)71-48)73-45-41(66)34(59)26(58)22-68-45/h10,24-48,54-67H,9,11-22H2,1-8H3
InChI KeyZXPNUZXGLAHYEE-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as triterpenoids. These are terpene molecules containing six isoprene units.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTriterpenoids
Direct ParentTriterpenoids
Alternative Parents
Substituents
  • Triterpenoid
  • Steroidal glycoside
  • Oligosaccharide
  • 12-hydroxysteroid
  • Hydroxysteroid
  • Steroid
  • Fatty acyl glycoside
  • Alkyl glycoside
  • Glycosyl compound
  • O-glycosyl compound
  • Oxane
  • Fatty acyl
  • Cyclic alcohol
  • Secondary alcohol
  • Polyol
  • Organoheterocyclic compound
  • Oxacycle
  • Acetal
  • Organooxygen compound
  • Alcohol
  • Hydrocarbon derivative
  • Organic oxygen compound
  • Primary 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 PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.98 g/LALOGPS
logP-0.07ALOGPS
logP-0.92ChemAxon
logS-3ALOGPS
pKa (Strongest Acidic)11.84ChemAxon
pKa (Strongest Basic)-3.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count22ChemAxon
Hydrogen Donor Count14ChemAxon
Polar Surface Area357.06 ŲChemAxon
Rotatable Bond Count15ChemAxon
Refractivity260.93 m³·mol⁻¹ChemAxon
Polarizability115.79 ųChemAxon
Number of Rings8ChemAxon
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]-346.73230932474
DeepCCS[M+Na]+320.79230932474
AllCCS[M+H]+323.332859911
AllCCS[M+H-H2O]+323.632859911
AllCCS[M+NH4]+323.032859911
AllCCS[M+Na]+322.932859911
AllCCS[M-H]-271.732859911
AllCCS[M+Na-2H]-278.432859911
AllCCS[M+HCOO]-285.732859911

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, 2022.6.07 minutes32390414
Predicted by Siyang on May 30, 202215.7774 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20223.98 minutes32390414
AjsUoB = Accucore 150 Amide HILIC with 10mM Ammonium Formate, 0.1% Formic Acid283.5 seconds40023050
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid3553.7 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid164.3 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid184.5 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid216.7 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid189.3 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid503.9 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 Acid696.0 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)735.8 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1099.5 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid598.2 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid1449.0 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid414.8 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid420.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate324.5 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA410.5 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water22.8 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra
Biological Properties
Cellular Locations
  • Cytoplasm
  • Extracellular
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 IDFDB020621
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound85106354
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 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. (). Yannai, Shmuel. (2004) Dictionary of food compounds with CD-ROM: Additives, flavors, and ingredients. Boca Raton: Chapman & Hall/CRC.. .
  6. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.