Hmdb loader

Showing metabocard for Columbaridione (HMDB0040388)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2012-09-12 01:55:00 UTC
Update Date2022-03-07 02:56:34 UTC
HMDB IDHMDB0040388
Secondary Accession Numbers
  • HMDB40388
Metabolite Identification
Common NameColumbaridione
DescriptionColumbaridione belongs to the class of organic compounds known as diterpene lactones. These are diterpenoids containing a lactone moiety. Columbaridione is an extremely weak basic (essentially neutral) compound (based on its pKa).
Structure
Data?1563863545
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0040388 (Columbaridione)


  Mrv0541 05061311482D          

 25 28  0  0  0  0            999 V2000
    7.0163    1.0217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9803   -0.4068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2497   -0.5444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1545   -1.0977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0679    1.1466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6375    0.4428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8926    1.1258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2509   -1.0274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5859    0.3179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0756   -1.0482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8566   -0.3027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7612    0.3387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5060   -0.3443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1117    0.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3308   -0.3651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3668    1.0633    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5421    1.0842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4227   -0.2799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0318   -0.2819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2870    0.4011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7251   -1.0898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7972    1.7672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1478    1.8088    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8375   -0.8548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9418   -0.4686    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  7  5  1  0  0  0  0
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
 10  8  1  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14 13  2  0  0  0  0
 15 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16 12  2  0  0  0  0
 17 14  1  0  0  0  0
 17 16  1  0  0  0  0
 19  3  1  0  0  0  0
 19  4  1  0  0  0  0
 19  6  1  0  0  0  0
 19 11  1  0  0  0  0
 20  7  1  0  0  0  0
 20 11  1  0  0  0  0
 20 14  1  0  0  0  0
 20 18  1  0  0  0  0
 21 15  2  0  0  0  0
 22 16  1  0  0  0  0
 23 17  2  0  0  0  0
 24 18  2  0  0  0  0
 18 25  1  0  0  0  0
 10 25  1  0  0  0  0
M  END
Download

3D MOL for HMDB0040388 (Columbaridione)

HMDB0040388
     RDKit          3D
Columbaridione
 49 52  0  0  0  0  0  0  0  0999 V2000
    5.3244   -0.7955   -1.0198 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4294    0.3163   -0.6262 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1432    1.1179    0.4646 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0627   -0.0116   -0.2636 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6092   -1.2432   -0.1595 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4963   -2.2728   -0.4128 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2112   -1.5063    0.2123 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8454   -2.7010    0.2929 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3262   -0.3907    0.4664 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7704    0.8673    0.3650 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1536    1.1241   -0.0030 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5796    2.3072   -0.1005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1901    1.9748    0.6381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3730    1.7850   -0.2714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7999    0.3579   -0.2333 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2710    0.2515   -0.2600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9927    0.7162    0.9462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7333    1.1261   -1.4382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6540   -1.1713   -0.5815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5678   -2.1649   -0.2744 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7565   -1.7514    0.9577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0994   -0.4665    0.8448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1890    0.3887    2.0831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6957   -0.1163    3.0987 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6888    1.6698    1.9579 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0102   -1.3636   -1.9195 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6534   -1.4477   -0.1734 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2944   -0.3073   -1.3474 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3942    1.0257   -1.5070 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7668    0.8562    1.4745 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2397    0.9482    0.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9777    2.2093    0.3257 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6200   -2.9524    0.3395 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2818    2.9467    0.5861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1761    2.4702    0.1056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0662    2.1362   -1.2907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4272   -0.1009   -1.1991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9159    1.2487    0.6347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3482   -0.0802    1.6306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3900    1.4853    1.4953 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6778    0.6577   -1.7941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0254    2.1428   -1.0761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9670    1.1590   -2.2337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8753   -1.2636   -1.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5935   -1.4203   -0.0458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0594   -3.1223   -0.0035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8896   -2.3406   -1.1067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5591   -1.6536    1.7611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2082   -2.6448    1.2428 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 10 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  2  0
 23 25  1  0
 11  4  1  0
 25 13  1  0
 22  9  1  0
 22 15  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  2 29  1  0
  3 30  1  0
  3 31  1  0
  3 32  1  0
  6 33  1  0
 13 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 17 38  1  0
 17 39  1  0
 17 40  1  0
 18 41  1  0
 18 42  1  0
 18 43  1  0
 19 44  1  0
 19 45  1  0
 20 46  1  0
 20 47  1  0
 21 48  1  0
 21 49  1  0
M  END
Download

3D SDF for HMDB0040388 (Columbaridione)


  Mrv0541 05061311482D          

 25 28  0  0  0  0            999 V2000
    7.0163    1.0217    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9803   -0.4068    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2497   -0.5444    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1545   -1.0977    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0679    1.1466    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6375    0.4428    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8926    1.1258    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2509   -1.0274    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5859    0.3179    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0756   -1.0482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8566   -0.3027    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7612    0.3387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5060   -0.3443    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.1117    0.3803    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3308   -0.3651    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3668    1.0633    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.5421    1.0842    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4227   -0.2799    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0318   -0.2819    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2870    0.4011    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.7251   -1.0898    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7972    1.7672    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1478    1.8088    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8375   -0.8548    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9418   -0.4686    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  6  5  1  0  0  0  0
  7  5  1  0  0  0  0
  9  1  1  0  0  0  0
  9  2  1  0  0  0  0
 10  8  1  0  0  0  0
 11  8  1  0  0  0  0
 12  9  1  0  0  0  0
 13 10  1  0  0  0  0
 14 13  2  0  0  0  0
 15 12  1  0  0  0  0
 15 13  1  0  0  0  0
 16 12  2  0  0  0  0
 17 14  1  0  0  0  0
 17 16  1  0  0  0  0
 19  3  1  0  0  0  0
 19  4  1  0  0  0  0
 19  6  1  0  0  0  0
 19 11  1  0  0  0  0
 20  7  1  0  0  0  0
 20 11  1  0  0  0  0
 20 14  1  0  0  0  0
 20 18  1  0  0  0  0
 21 15  2  0  0  0  0
 22 16  1  0  0  0  0
 23 17  2  0  0  0  0
 24 18  2  0  0  0  0
 18 25  1  0  0  0  0
 10 25  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0040388

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)C1=C(O)C(=O)C2=C(C3CC4C(C)(C)CCCC24C(=O)O3)C1=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H24O5/c1-9(2)12-15(21)13-10-8-11-19(3,4)6-5-7-20(11,18(24)25-10)14(13)17(23)16(12)22/h9-11,22H,5-8H2,1-4H3

> <INCHI_KEY>
ZGIOOTXNBWWRKD-UHFFFAOYSA-N

> <FORMULA>
C20H24O5

> <MOLECULAR_WEIGHT>
344.4016

> <EXACT_MASS>
344.162373878

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
36.46052079480931

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
4-hydroxy-11,11-dimethyl-5-(propan-2-yl)-16-oxatetracyclo[6.6.2.0¹,¹⁰.0²,⁷]hexadeca-2(7),4-diene-3,6,15-trione

> <ALOGPS_LOGP>
2.58

> <JCHEM_LOGP>
3.361022399666666

> <ALOGPS_LOGS>
-3.81

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA_STRONGEST_ACIDIC>
8.313823755185718

> <JCHEM_PKA_STRONGEST_BASIC>
-4.091793489481767

> <JCHEM_POLAR_SURFACE_AREA>
80.67

> <JCHEM_REFRACTIVITY>
92.35319999999996

> <JCHEM_ROTATABLE_BOND_COUNT>
1

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.36e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
4-hydroxy-5-isopropyl-11,11-dimethyl-16-oxatetracyclo[6.6.2.0¹,¹⁰.0²,⁷]hexadeca-2(7),4-diene-3,6,15-trione

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0040388 (Columbaridione)

HMDB0040388
     RDKit          3D
Columbaridione
 49 52  0  0  0  0  0  0  0  0999 V2000
    5.3244   -0.7955   -1.0198 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4294    0.3163   -0.6262 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1432    1.1179    0.4646 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0627   -0.0116   -0.2636 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6092   -1.2432   -0.1595 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4963   -2.2728   -0.4128 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2112   -1.5063    0.2123 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8454   -2.7010    0.2929 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3262   -0.3907    0.4664 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7704    0.8673    0.3650 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1536    1.1241   -0.0030 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5796    2.3072   -0.1005 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1901    1.9748    0.6381 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3730    1.7850   -0.2714 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7999    0.3579   -0.2333 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2710    0.2515   -0.2600 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9927    0.7162    0.9462 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7333    1.1261   -1.4382 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6540   -1.1713   -0.5815 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5678   -2.1649   -0.2744 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7565   -1.7514    0.9577 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0994   -0.4665    0.8448 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.1890    0.3887    2.0831 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6957   -0.1163    3.0987 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6888    1.6698    1.9579 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0102   -1.3636   -1.9195 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6534   -1.4477   -0.1734 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2944   -0.3073   -1.3474 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3942    1.0257   -1.5070 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7668    0.8562    1.4745 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2397    0.9482    0.4124 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9777    2.2093    0.3257 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6200   -2.9524    0.3395 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2818    2.9467    0.5861 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1761    2.4702    0.1056 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0662    2.1362   -1.2907 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4272   -0.1009   -1.1991 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9159    1.2487    0.6347 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3482   -0.0802    1.6306 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3900    1.4853    1.4953 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6778    0.6577   -1.7941 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0254    2.1428   -1.0761 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9670    1.1590   -2.2337 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8753   -1.2636   -1.6642 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5935   -1.4203   -0.0458 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0594   -3.1223   -0.0035 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8896   -2.3406   -1.1067 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5591   -1.6536    1.7611 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2082   -2.6448    1.2428 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  5  7  1  0
  7  8  2  0
  7  9  1  0
  9 10  2  0
 10 11  1  0
 11 12  2  0
 10 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 16 18  1  0
 16 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  2  0
 23 25  1  0
 11  4  1  0
 25 13  1  0
 22  9  1  0
 22 15  1  0
  1 26  1  0
  1 27  1  0
  1 28  1  0
  2 29  1  0
  3 30  1  0
  3 31  1  0
  3 32  1  0
  6 33  1  0
 13 34  1  0
 14 35  1  0
 14 36  1  0
 15 37  1  0
 17 38  1  0
 17 39  1  0
 17 40  1  0
 18 41  1  0
 18 42  1  0
 18 43  1  0
 19 44  1  0
 19 45  1  0
 20 46  1  0
 20 47  1  0
 21 48  1  0
 21 49  1  0
M  END
Download

PDB for HMDB0040388 (Columbaridione)

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      13.097   1.907   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      13.030  -0.759   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.333  -1.016   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       4.022  -2.049   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       3.860   2.140   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       3.057   0.827   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.400   2.101   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.068  -1.918   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      12.294   0.593   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       7.608  -1.957   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.332  -0.565   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      10.754   0.632   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0       8.411  -0.643   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       7.675   0.710   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       9.951  -0.682   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.018   1.985   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0       8.479   2.024   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0       6.389  -0.522   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       3.793  -0.526   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       6.136   0.749   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      10.687  -2.034   0.000  0.00  0.00           O+0
HETATM   22  O   UNK     0      10.821   3.299   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       7.743   3.376   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       5.297  -1.596   0.000  0.00  0.00           O+0
HETATM   25  O   UNK     0       7.358  -0.875   0.000  0.00  0.00           O+0
CONECT    1    9                                                            
CONECT    2    9                                                            
CONECT    3   19                                                            
CONECT    4   19                                                            
CONECT    5    6    7                                                       
CONECT    6    5   19                                                       
CONECT    7    5   20                                                       
CONECT    8   10   11                                                       
CONECT    9    1    2   12                                                  
CONECT   10    8   13   25                                                  
CONECT   11    8   19   20                                                  
CONECT   12    9   15   16                                                  
CONECT   13   10   14   15                                                  
CONECT   14   13   17   20                                                  
CONECT   15   12   13   21                                                  
CONECT   16   12   17   22                                                  
CONECT   17   14   16   23                                                  
CONECT   18   20   24   25                                                  
CONECT   19    3    4    6   11                                             
CONECT   20    7   11   14   18                                             
CONECT   21   15                                                            
CONECT   22   16                                                            
CONECT   23   17                                                            
CONECT   24   18                                                            
CONECT   25   18   10                                                       
MASTER        0    0    0    0    0    0    0    0   25    0   56    0
END
Download

3D PDB for HMDB0040388 (Columbaridione)

COMPND    HMDB0040388
HETATM    1  C1  UNL     1       5.324  -0.796  -1.020  1.00  0.00           C  
HETATM    2  C2  UNL     1       4.429   0.316  -0.626  1.00  0.00           C  
HETATM    3  C3  UNL     1       5.143   1.118   0.465  1.00  0.00           C  
HETATM    4  C4  UNL     1       3.063  -0.012  -0.264  1.00  0.00           C  
HETATM    5  C5  UNL     1       2.609  -1.243  -0.160  1.00  0.00           C  
HETATM    6  O1  UNL     1       3.496  -2.273  -0.413  1.00  0.00           O  
HETATM    7  C6  UNL     1       1.211  -1.506   0.212  1.00  0.00           C  
HETATM    8  O2  UNL     1       0.845  -2.701   0.293  1.00  0.00           O  
HETATM    9  C7  UNL     1       0.326  -0.391   0.466  1.00  0.00           C  
HETATM   10  C8  UNL     1       0.770   0.867   0.365  1.00  0.00           C  
HETATM   11  C9  UNL     1       2.154   1.124  -0.003  1.00  0.00           C  
HETATM   12  O3  UNL     1       2.580   2.307  -0.100  1.00  0.00           O  
HETATM   13  C10 UNL     1      -0.190   1.975   0.638  1.00  0.00           C  
HETATM   14  C11 UNL     1      -1.373   1.785  -0.271  1.00  0.00           C  
HETATM   15  C12 UNL     1      -1.800   0.358  -0.233  1.00  0.00           C  
HETATM   16  C13 UNL     1      -3.271   0.252  -0.260  1.00  0.00           C  
HETATM   17  C14 UNL     1      -3.993   0.716   0.946  1.00  0.00           C  
HETATM   18  C15 UNL     1      -3.733   1.126  -1.438  1.00  0.00           C  
HETATM   19  C16 UNL     1      -3.654  -1.171  -0.581  1.00  0.00           C  
HETATM   20  C17 UNL     1      -2.568  -2.165  -0.274  1.00  0.00           C  
HETATM   21  C18 UNL     1      -1.756  -1.751   0.958  1.00  0.00           C  
HETATM   22  C19 UNL     1      -1.099  -0.467   0.845  1.00  0.00           C  
HETATM   23  C20 UNL     1      -1.189   0.389   2.083  1.00  0.00           C  
HETATM   24  O4  UNL     1      -1.696  -0.116   3.099  1.00  0.00           O  
HETATM   25  O5  UNL     1      -0.689   1.670   1.958  1.00  0.00           O  
HETATM   26  H1  UNL     1       5.010  -1.364  -1.919  1.00  0.00           H  
HETATM   27  H2  UNL     1       5.653  -1.448  -0.173  1.00  0.00           H  
HETATM   28  H3  UNL     1       6.294  -0.307  -1.347  1.00  0.00           H  
HETATM   29  H4  UNL     1       4.394   1.026  -1.507  1.00  0.00           H  
HETATM   30  H5  UNL     1       4.767   0.856   1.475  1.00  0.00           H  
HETATM   31  H6  UNL     1       6.240   0.948   0.412  1.00  0.00           H  
HETATM   32  H7  UNL     1       4.978   2.209   0.326  1.00  0.00           H  
HETATM   33  H8  UNL     1       3.620  -2.952   0.340  1.00  0.00           H  
HETATM   34  H9  UNL     1       0.282   2.947   0.586  1.00  0.00           H  
HETATM   35  H10 UNL     1      -2.176   2.470   0.106  1.00  0.00           H  
HETATM   36  H11 UNL     1      -1.066   2.136  -1.291  1.00  0.00           H  
HETATM   37  H12 UNL     1      -1.427  -0.101  -1.199  1.00  0.00           H  
HETATM   38  H13 UNL     1      -4.916   1.249   0.635  1.00  0.00           H  
HETATM   39  H14 UNL     1      -4.348  -0.080   1.631  1.00  0.00           H  
HETATM   40  H15 UNL     1      -3.390   1.485   1.495  1.00  0.00           H  
HETATM   41  H16 UNL     1      -4.678   0.658  -1.794  1.00  0.00           H  
HETATM   42  H17 UNL     1      -4.025   2.143  -1.076  1.00  0.00           H  
HETATM   43  H18 UNL     1      -2.967   1.159  -2.234  1.00  0.00           H  
HETATM   44  H19 UNL     1      -3.875  -1.264  -1.664  1.00  0.00           H  
HETATM   45  H20 UNL     1      -4.593  -1.420  -0.046  1.00  0.00           H  
HETATM   46  H21 UNL     1      -3.059  -3.122  -0.004  1.00  0.00           H  
HETATM   47  H22 UNL     1      -1.890  -2.341  -1.107  1.00  0.00           H  
HETATM   48  H23 UNL     1      -2.559  -1.654   1.761  1.00  0.00           H  
HETATM   49  H24 UNL     1      -1.208  -2.645   1.243  1.00  0.00           H  
CONECT    1    2   26   27   28
CONECT    2    3    4   29
CONECT    3   30   31   32
CONECT    4    5    5   11
CONECT    5    6    7
CONECT    6   33
CONECT    7    8    8    9
CONECT    9   10   10   22
CONECT   10   11   13
CONECT   11   12   12
CONECT   13   14   25   34
CONECT   14   15   35   36
CONECT   15   16   22   37
CONECT   16   17   18   19
CONECT   17   38   39   40
CONECT   18   41   42   43
CONECT   19   20   44   45
CONECT   20   21   46   47
CONECT   21   22   48   49
CONECT   22   23
CONECT   23   24   24   25
END
Download

SMILES for HMDB0040388 (Columbaridione)

CC(C)C1=C(O)C(=O)C2=C(C3CC4C(C)(C)CCCC24C(=O)O3)C1=O
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INCHI for HMDB0040388 (Columbaridione)

InChI=1S/C20H24O5/c1-9(2)12-15(21)13-10-8-11-19(3,4)6-5-7-20(11,18(24)25-10)14(13)17(23)16(12)22/h9-11,22H,5-8H2,1-4H3
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View in JSmolView Stereo Labels
SynonymsNot Available
Chemical FormulaC20H24O5
Average Molecular Weight344.4016
Monoisotopic Molecular Weight344.162373878
IUPAC Name4-hydroxy-11,11-dimethyl-5-(propan-2-yl)-16-oxatetracyclo[6.6.2.0¹,¹⁰.0²,⁷]hexadeca-2(7),4-diene-3,6,15-trione
Traditional Name4-hydroxy-5-isopropyl-11,11-dimethyl-16-oxatetracyclo[6.6.2.0¹,¹⁰.0²,⁷]hexadeca-2(7),4-diene-3,6,15-trione
CAS Registry Number156162-09-3
SMILES
CC(C)C1=C(O)C(=O)C2=C(C3CC4C(C)(C)CCCC24C(=O)O3)C1=O
InChI Identifier
InChI=1S/C20H24O5/c1-9(2)12-15(21)13-10-8-11-19(3,4)6-5-7-20(11,18(24)25-10)14(13)17(23)16(12)22/h9-11,22H,5-8H2,1-4H3
InChI KeyZGIOOTXNBWWRKD-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as diterpene lactones. These are diterpenoids containing a lactone moiety.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassPrenol lipids
Sub ClassTerpene lactones
Direct ParentDiterpene lactones
Alternative ParentsNot Available
SubstituentsNot Available
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
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
Water Solubility0.054 g/LALOGPS
logP2.58ALOGPS
logP3.36ChemAxon
logS-3.8ALOGPS
pKa (Strongest Acidic)8.31ChemAxon
pKa (Strongest Basic)-4.1ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count4ChemAxon
Hydrogen Donor Count1ChemAxon
Polar Surface Area80.67 ŲChemAxon
Rotatable Bond Count1ChemAxon
Refractivity92.35 m³·mol⁻¹ChemAxon
Polarizability36.46 ųChemAxon
Number of Rings4ChemAxon
BioavailabilityYesChemAxon
Rule of FiveYesChemAxon
Ghose FilterYesChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
DarkChem[M+H]+177.99231661259
DarkChem[M-H]-176.87231661259
DeepCCS[M-2H]-222.86430932474
DeepCCS[M+Na]+198.09230932474
AllCCS[M+H]+180.232859911
AllCCS[M+H-H2O]+177.432859911
AllCCS[M+NH4]+182.932859911
AllCCS[M+Na]+183.632859911
AllCCS[M-H]-189.132859911
AllCCS[M+Na-2H]-189.232859911
AllCCS[M+HCOO]-189.432859911

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
ColumbaridioneCC(C)C1=C(O)C(=O)C2=C(C3CC4C(C)(C)CCCC24C(=O)O3)C1=O3761.4Standard polar33892256
ColumbaridioneCC(C)C1=C(O)C(=O)C2=C(C3CC4C(C)(C)CCCC24C(=O)O3)C1=O2289.5Standard non polar33892256
ColumbaridioneCC(C)C1=C(O)C(=O)C2=C(C3CC4C(C)(C)CCCC24C(=O)O3)C1=O2637.9Semi standard non polar33892256

Derivatized

Derivative Name / StructureSMILESKovats RI ValueColumn TypeReference
Columbaridione,1TMS,isomer #1CC(C)C1=C(O[Si](C)(C)C)C(=O)C2=C(C1=O)C1CC3C(C)(C)CCCC23C(=O)O12841.2Semi standard non polar33892256
Columbaridione,1TBDMS,isomer #1CC(C)C1=C(O[Si](C)(C)C(C)(C)C)C(=O)C2=C(C1=O)C1CC3C(C)(C)CCCC23C(=O)O13097.3Semi standard non polar33892256
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted GC-MSPredicted GC-MS Spectrum - Columbaridione GC-MS (Non-derivatized) - 70eV, Positivesplash10-00o0-9126000000-6e7b2fdecdffaa3518112017-09-01Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Columbaridione GC-MS (1 TMS) - 70eV, Positivesplash10-0fz9-9203200000-3c7a788bc1478a7e761e2017-10-06Wishart LabView Spectrum
Predicted GC-MSPredicted GC-MS Spectrum - Columbaridione GC-MS (Non-derivatized) - 70eV, PositiveNot Available2021-10-12Wishart LabView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Columbaridione 10V, Positive-QTOFsplash10-0002-0009000000-7a658243e0ed005f72b12017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Columbaridione 20V, Positive-QTOFsplash10-054k-6159000000-de40f5f8149471cd94ff2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Columbaridione 40V, Positive-QTOFsplash10-0a4i-9230000000-637db58b568a487048f82017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Columbaridione 10V, Negative-QTOFsplash10-0006-0009000000-32ec3a51eebfc8d00d8f2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Columbaridione 20V, Negative-QTOFsplash10-0006-0019000000-be4db0a667be2dcfbf5c2017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Columbaridione 40V, Negative-QTOFsplash10-0540-6792000000-37bcf3c9155f02cd43d72017-09-01Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Columbaridione 10V, Positive-QTOFsplash10-0002-0009000000-70d92b3e026609570d4a2021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Columbaridione 20V, Positive-QTOFsplash10-0002-0019000000-6c3ce8c5aa5405f68b722021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Columbaridione 40V, Positive-QTOFsplash10-000t-9063000000-99056fddb7a5436d21642021-09-23Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Columbaridione 10V, Negative-QTOFsplash10-0006-0009000000-4fdd89030f0f4a9209ed2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Columbaridione 20V, Negative-QTOFsplash10-0006-0009000000-4fdd89030f0f4a9209ed2021-09-24Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Columbaridione 40V, Negative-QTOFsplash10-0006-1049000000-774cc3eb27de400c46a32021-09-24Wishart LabView Spectrum
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB020120
KNApSAcK IDC00036922
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem CompoundNot Available
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 ]
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