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Showing metabocard for 5,6-Dihydroxyprostaglandin F1a (HMDB0012109)

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Record Information
Version5.0
StatusExpected but not Quantified
Creation Date2009-04-02 17:25:00 UTC
Update Date2022-03-07 02:51:21 UTC
HMDB IDHMDB0012109
Secondary Accession Numbers
  • HMDB12109
Metabolite Identification
Common Name5,6-Dihydroxyprostaglandin F1a
DescriptionProstaglandins are eicosanoids. The eicosanoids consist of the prostaglandins (PGs), thromboxanes (TXs), leukotrienes (LTs), and lipoxins (LXs). The PGs and TXs are collectively identified as prostanoids. Prostaglandins were originally shown to be synthesized in the prostate gland, thromboxanes from platelets (thrombocytes), and leukotrienes from leukocytes, hence the derivation of their names. All mammalian cells except erythrocytes synthesize eicosanoids. These molecules are extremely potent, able to cause profound physiological effects at very dilute concentrations. All eicosanoids function locally at the site of synthesis, through receptor-mediated G-protein linked signalling pathways.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0012109 (5,6-Dihydroxyprostaglandin F1a)

  Mrv0541 02241203392D          

 27 27  0  0  1  0            999 V2000
   20.7863  -12.3409    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.4393  -11.1597    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.5814   -8.2119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5974  -10.9684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3118   -9.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.3131  -10.9684    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.0668  -10.6328    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   21.3994  -11.7889    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.6189  -11.2459    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   22.2064  -11.9604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.5987  -10.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.2383   -9.8259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.8842  -10.9684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0230   -9.5709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1697  -10.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.1945   -8.7640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.4553  -10.9684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9791   -8.5090    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.1506   -7.7020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7408  -10.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.9353   -7.4471    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0263  -10.9684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.1068   -6.6401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.8914   -6.3852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3118  -10.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1697   -9.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.8842  -11.7934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  6  0  0  0
  9  2  1  6  0  0  0
 16  3  1  1  0  0  0
  4 25  1  0  0  0  0
  5 25  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6 11  1  6  0  0  0
  7  9  1  0  0  0  0
  7 12  1  1  0  0  0
  8 10  1  0  0  0  0
  9 10  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  2  0  0  0  0
 13 15  1  0  0  0  0
 14 16  1  0  0  0  0
 15 17  1  0  0  0  0
 16 18  1  0  0  0  0
 17 20  1  0  0  0  0
 18 19  1  0  0  0  0
 19 21  1  0  0  0  0
 20 22  1  0  0  0  0
 21 23  1  0  0  0  0
 22 25  1  0  0  0  0
 23 24  1  0  0  0  0
 15 26  1  0  0  0  0
 13 27  1  0  0  0  0
M  END
Download

3D MOL for HMDB0012109 (5,6-Dihydroxyprostaglandin F1a)

HMDB0012109
     RDKit          3D
5,6-Dihydroxyprostaglandin F1a
 63 63  0  0  0  0  0  0  0  0999 V2000
    4.0945    3.5906   -2.0538 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2003    3.5606   -0.8528 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5826    2.4722    0.1267 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5076    1.0926   -0.5114 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9184    0.1085    0.5923 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8842   -1.3168    0.0798 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7933   -1.3692   -0.9907 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5546   -1.7152   -0.3925 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6179   -2.2716    0.3760 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2748   -2.6655   -0.1352 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0688   -4.1249    0.2203 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2656   -4.8739   -0.9054 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9885   -4.1816    1.2837 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9768   -2.7629    1.8487 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0756   -2.4854    2.6245 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8376   -1.9167    0.6127 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0593   -1.9087   -0.2527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2685   -1.2369    0.2945 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3284   -1.3382   -0.6794 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0988    0.2322    0.5761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1364    0.4182    1.5414 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7469    0.9203   -0.7269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5560    2.4109   -0.5526 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7746    3.1000   -0.0345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4626    4.5473    0.0924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3396    5.0252   -0.2077 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4264    5.4566    0.5609 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2098    4.6356   -2.3795 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1193    3.2169   -1.8021 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6812    3.0097   -2.9131 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2925    4.5193   -0.3221 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1530    3.4766   -1.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6051    2.6634    0.4584 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8343    2.4904    0.9377 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5057    0.8851   -0.8891 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2160    1.0163   -1.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9524    0.3985    0.8679 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2895    0.2550    1.4934 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2998   -1.9558    0.8688 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3375   -1.2701   -1.8685 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2669   -1.5641   -1.4422 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8485   -2.4430    1.4185 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1650   -2.4790   -1.2039 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9961   -4.5828    0.6346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2593   -5.7107   -0.9726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7069   -4.9206    2.0711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9869   -4.4590    0.9141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0203   -2.6909    2.4112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4563   -3.3412    2.9694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4985   -0.8962    0.8462 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2947   -2.9994   -0.4765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8382   -1.5028   -1.2787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6923   -1.7000    1.1896 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6747   -2.2696   -0.6616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0499    0.6257    0.9998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5516    1.1888    1.3949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7782    0.5161   -1.0643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4912    0.7341   -1.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3808    2.8075   -1.5957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6767    2.6902    0.0252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6131    3.0154   -0.7822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1024    2.7508    0.9507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3746    5.1221    0.7240 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  2  0
 25 27  1  0
 16 10  1  0
  1 28  1  0
  1 29  1  0
  1 30  1  0
  2 31  1  0
  2 32  1  0
  3 33  1  0
  3 34  1  0
  4 35  1  0
  4 36  1  0
  5 37  1  0
  5 38  1  0
  6 39  1  1
  7 40  1  0
  8 41  1  0
  9 42  1  0
 10 43  1  6
 11 44  1  1
 12 45  1  0
 13 46  1  0
 13 47  1  0
 14 48  1  1
 15 49  1  0
 16 50  1  1
 17 51  1  0
 17 52  1  0
 18 53  1  0
 19 54  1  0
 20 55  1  0
 21 56  1  0
 22 57  1  0
 22 58  1  0
 23 59  1  0
 23 60  1  0
 24 61  1  0
 24 62  1  0
 27 63  1  0
M  END
Download

3D SDF for HMDB0012109 (5,6-Dihydroxyprostaglandin F1a)

  Mrv0541 02241203392D          

 27 27  0  0  1  0            999 V2000
   20.7863  -12.3409    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.4393  -11.1597    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.5814   -8.2119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.5974  -10.9684    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3118   -9.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.3131  -10.9684    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.0668  -10.6328    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   21.3994  -11.7889    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.6189  -11.2459    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   22.2064  -11.9604    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.5987  -10.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.2383   -9.8259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.8842  -10.9684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.0230   -9.5709    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1697  -10.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.1945   -8.7640    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   18.4553  -10.9684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9791   -8.5090    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.1506   -7.7020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7408  -10.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.9353   -7.4471    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0263  -10.9684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.1068   -6.6401    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.8914   -6.3852    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3118  -10.5559    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1697   -9.7309    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.8842  -11.7934    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  8  1  1  6  0  0  0
  9  2  1  6  0  0  0
 16  3  1  1  0  0  0
  4 25  1  0  0  0  0
  5 25  2  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6 11  1  6  0  0  0
  7  9  1  0  0  0  0
  7 12  1  1  0  0  0
  8 10  1  0  0  0  0
  9 10  1  0  0  0  0
 11 13  1  0  0  0  0
 12 14  2  0  0  0  0
 13 15  1  0  0  0  0
 14 16  1  0  0  0  0
 15 17  1  0  0  0  0
 16 18  1  0  0  0  0
 17 20  1  0  0  0  0
 18 19  1  0  0  0  0
 19 21  1  0  0  0  0
 20 22  1  0  0  0  0
 21 23  1  0  0  0  0
 22 25  1  0  0  0  0
 23 24  1  0  0  0  0
 15 26  1  0  0  0  0
 13 27  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0012109

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC[C@H](O)\C=C\[C@H]1[C@H](O)C[C@H](O)[C@@H]1CC(O)C(O)CCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C20H36O7/c1-2-3-4-6-13(21)9-10-14-15(18(24)12-17(14)23)11-19(25)16(22)7-5-8-20(26)27/h9-10,13-19,21-25H,2-8,11-12H2,1H3,(H,26,27)/b10-9+/t13-,14+,15+,16?,17+,18-,19?/m0/s1

> <INCHI_KEY>
SAAOVBGAFHJPIF-NYNACFBQSA-N

> <FORMULA>
C20H36O7

> <MOLECULAR_WEIGHT>
388.4956

> <EXACT_MASS>
388.246103506

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
44.112408967232014

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
7-[(1R,2R,3R,5S)-3,5-dihydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]cyclopentyl]-5,6-dihydroxyheptanoic acid

> <ALOGPS_LOGP>
1.14

> <JCHEM_LOGP>
0.5113539399999993

> <ALOGPS_LOGS>
-2.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.807784416932432

> <JCHEM_PKA_STRONGEST_ACIDIC>
4.136274044037547

> <JCHEM_PKA_STRONGEST_BASIC>
-1.6263155845122892

> <JCHEM_POLAR_SURFACE_AREA>
138.45000000000002

> <JCHEM_REFRACTIVITY>
102.3851

> <JCHEM_ROTATABLE_BOND_COUNT>
13

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.40e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
7-[(1R,2R,3R,5S)-3,5-dihydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]cyclopentyl]-5,6-dihydroxyheptanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0012109 (5,6-Dihydroxyprostaglandin F1a)

HMDB0012109
     RDKit          3D
5,6-Dihydroxyprostaglandin F1a
 63 63  0  0  0  0  0  0  0  0999 V2000
    4.0945    3.5906   -2.0538 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2003    3.5606   -0.8528 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5826    2.4722    0.1267 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5076    1.0926   -0.5114 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9184    0.1085    0.5923 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8842   -1.3168    0.0798 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.7933   -1.3692   -0.9907 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5546   -1.7152   -0.3925 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6179   -2.2716    0.3760 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2748   -2.6655   -0.1352 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0688   -4.1249    0.2203 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.2656   -4.8739   -0.9054 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9885   -4.1816    1.2837 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9768   -2.7629    1.8487 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0756   -2.4854    2.6245 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8376   -1.9167    0.6127 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.0593   -1.9087   -0.2527 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2685   -1.2369    0.2945 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.3284   -1.3382   -0.6794 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0988    0.2322    0.5761 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1364    0.4182    1.5414 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7469    0.9203   -0.7269 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5560    2.4109   -0.5526 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7746    3.1000   -0.0345 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4626    4.5473    0.0924 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3396    5.0252   -0.2077 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4264    5.4566    0.5609 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2098    4.6356   -2.3795 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.1193    3.2169   -1.8021 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6812    3.0097   -2.9131 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2925    4.5193   -0.3221 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1530    3.4766   -1.2005 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6051    2.6634    0.4584 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8343    2.4904    0.9377 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.5057    0.8851   -0.8891 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2160    1.0163   -1.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9524    0.3985    0.8679 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2895    0.2550    1.4934 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2998   -1.9558    0.8688 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3375   -1.2701   -1.8685 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2669   -1.5641   -1.4422 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8485   -2.4430    1.4185 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1650   -2.4790   -1.2039 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9961   -4.5828    0.6346 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2593   -5.7107   -0.9726 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7069   -4.9206    2.0711 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9869   -4.4590    0.9141 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0203   -2.6909    2.4112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4563   -3.3412    2.9694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4985   -0.8962    0.8462 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2947   -2.9994   -0.4765 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8382   -1.5028   -1.2787 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6923   -1.7000    1.1896 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6747   -2.2696   -0.6616 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0499    0.6257    0.9998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5516    1.1888    1.3949 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7782    0.5161   -1.0643 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4912    0.7341   -1.5065 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3808    2.8075   -1.5957 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6767    2.6902    0.0252 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6131    3.0154   -0.7822 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1024    2.7508    0.9507 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.3746    5.1221    0.7240 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  6  8  1  0
  8  9  2  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 14 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 18 20  1  0
 20 21  1  0
 20 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  2  0
 25 27  1  0
 16 10  1  0
  1 28  1  0
  1 29  1  0
  1 30  1  0
  2 31  1  0
  2 32  1  0
  3 33  1  0
  3 34  1  0
  4 35  1  0
  4 36  1  0
  5 37  1  0
  5 38  1  0
  6 39  1  1
  7 40  1  0
  8 41  1  0
  9 42  1  0
 10 43  1  6
 11 44  1  1
 12 45  1  0
 13 46  1  0
 13 47  1  0
 14 48  1  1
 15 49  1  0
 16 50  1  1
 17 51  1  0
 17 52  1  0
 18 53  1  0
 19 54  1  0
 20 55  1  0
 21 56  1  0
 22 57  1  0
 22 58  1  0
 23 59  1  0
 23 60  1  0
 24 61  1  0
 24 62  1  0
 27 63  1  0
M  END
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PDB for HMDB0012109 (5,6-Dihydroxyprostaglandin F1a)

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  O   UNK     0      38.801 -23.036   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      43.753 -20.831   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      42.152 -15.329   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      29.115 -20.474   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      30.449 -18.164   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      39.784 -20.474   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      41.191 -19.848   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      39.946 -22.006   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      42.222 -20.992   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      41.452 -22.326   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      38.451 -19.704   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      41.511 -18.342   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      37.117 -20.474   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      42.976 -17.866   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      35.783 -19.704   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      43.296 -16.359   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      34.450 -20.474   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      44.761 -15.883   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      45.081 -14.377   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      33.116 -19.704   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      46.546 -13.901   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      31.782 -20.474   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      46.866 -12.395   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      48.331 -11.919   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      30.449 -19.704   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      35.783 -18.164   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      37.117 -22.014   0.000  0.00  0.00           O+0
CONECT    1    8                                                            
CONECT    2    9                                                            
CONECT    3   16                                                            
CONECT    4   25                                                            
CONECT    5   25                                                            
CONECT    6    7    8   11                                                  
CONECT    7    6    9   12                                                  
CONECT    8    1    6   10                                                  
CONECT    9    2    7   10                                                  
CONECT   10    8    9                                                       
CONECT   11    6   13                                                       
CONECT   12    7   14                                                       
CONECT   13   11   15   27                                                  
CONECT   14   12   16                                                       
CONECT   15   13   17   26                                                  
CONECT   16    3   14   18                                                  
CONECT   17   15   20                                                       
CONECT   18   16   19                                                       
CONECT   19   18   21                                                       
CONECT   20   17   22                                                       
CONECT   21   19   23                                                       
CONECT   22   20   25                                                       
CONECT   23   21   24                                                       
CONECT   24   23                                                            
CONECT   25    4    5   22                                                  
CONECT   26   15                                                            
CONECT   27   13                                                            
MASTER        0    0    0    0    0    0    0    0   27    0   54    0
END
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3D PDB for HMDB0012109 (5,6-Dihydroxyprostaglandin F1a)

COMPND    HMDB0012109
HETATM    1  C1  UNL     1       4.095   3.591  -2.054  1.00  0.00           C  
HETATM    2  C2  UNL     1       3.200   3.561  -0.853  1.00  0.00           C  
HETATM    3  C3  UNL     1       3.583   2.472   0.127  1.00  0.00           C  
HETATM    4  C4  UNL     1       3.508   1.093  -0.511  1.00  0.00           C  
HETATM    5  C5  UNL     1       3.918   0.109   0.592  1.00  0.00           C  
HETATM    6  C6  UNL     1       3.884  -1.317   0.080  1.00  0.00           C  
HETATM    7  O1  UNL     1       4.793  -1.369  -0.991  1.00  0.00           O  
HETATM    8  C7  UNL     1       2.555  -1.715  -0.393  1.00  0.00           C  
HETATM    9  C8  UNL     1       1.618  -2.272   0.376  1.00  0.00           C  
HETATM   10  C9  UNL     1       0.275  -2.665  -0.135  1.00  0.00           C  
HETATM   11  C10 UNL     1       0.069  -4.125   0.220  1.00  0.00           C  
HETATM   12  O2  UNL     1      -0.266  -4.874  -0.905  1.00  0.00           O  
HETATM   13  C11 UNL     1      -0.988  -4.182   1.284  1.00  0.00           C  
HETATM   14  C12 UNL     1      -0.977  -2.763   1.849  1.00  0.00           C  
HETATM   15  O3  UNL     1      -2.076  -2.485   2.624  1.00  0.00           O  
HETATM   16  C13 UNL     1      -0.838  -1.917   0.613  1.00  0.00           C  
HETATM   17  C14 UNL     1      -2.059  -1.909  -0.253  1.00  0.00           C  
HETATM   18  C15 UNL     1      -3.268  -1.237   0.294  1.00  0.00           C  
HETATM   19  O4  UNL     1      -4.328  -1.338  -0.679  1.00  0.00           O  
HETATM   20  C16 UNL     1      -3.099   0.232   0.576  1.00  0.00           C  
HETATM   21  O5  UNL     1      -2.136   0.418   1.541  1.00  0.00           O  
HETATM   22  C17 UNL     1      -2.747   0.920  -0.727  1.00  0.00           C  
HETATM   23  C18 UNL     1      -2.556   2.411  -0.553  1.00  0.00           C  
HETATM   24  C19 UNL     1      -3.775   3.100  -0.034  1.00  0.00           C  
HETATM   25  C20 UNL     1      -3.463   4.547   0.092  1.00  0.00           C  
HETATM   26  O6  UNL     1      -2.340   5.025  -0.208  1.00  0.00           O  
HETATM   27  O7  UNL     1      -4.426   5.457   0.561  1.00  0.00           O  
HETATM   28  H1  UNL     1       4.210   4.636  -2.379  1.00  0.00           H  
HETATM   29  H2  UNL     1       5.119   3.217  -1.802  1.00  0.00           H  
HETATM   30  H3  UNL     1       3.681   3.010  -2.913  1.00  0.00           H  
HETATM   31  H4  UNL     1       3.293   4.519  -0.322  1.00  0.00           H  
HETATM   32  H5  UNL     1       2.153   3.477  -1.200  1.00  0.00           H  
HETATM   33  H6  UNL     1       4.605   2.663   0.458  1.00  0.00           H  
HETATM   34  H7  UNL     1       2.834   2.490   0.938  1.00  0.00           H  
HETATM   35  H8  UNL     1       2.506   0.885  -0.889  1.00  0.00           H  
HETATM   36  H9  UNL     1       4.216   1.016  -1.350  1.00  0.00           H  
HETATM   37  H10 UNL     1       4.952   0.398   0.868  1.00  0.00           H  
HETATM   38  H11 UNL     1       3.289   0.255   1.493  1.00  0.00           H  
HETATM   39  H12 UNL     1       4.300  -1.956   0.869  1.00  0.00           H  
HETATM   40  H13 UNL     1       4.338  -1.270  -1.869  1.00  0.00           H  
HETATM   41  H14 UNL     1       2.267  -1.564  -1.442  1.00  0.00           H  
HETATM   42  H15 UNL     1       1.849  -2.443   1.418  1.00  0.00           H  
HETATM   43  H16 UNL     1       0.165  -2.479  -1.204  1.00  0.00           H  
HETATM   44  H17 UNL     1       0.996  -4.583   0.635  1.00  0.00           H  
HETATM   45  H18 UNL     1       0.259  -5.711  -0.973  1.00  0.00           H  
HETATM   46  H19 UNL     1      -0.707  -4.921   2.071  1.00  0.00           H  
HETATM   47  H20 UNL     1      -1.987  -4.459   0.914  1.00  0.00           H  
HETATM   48  H21 UNL     1      -0.020  -2.691   2.411  1.00  0.00           H  
HETATM   49  H22 UNL     1      -2.456  -3.341   2.969  1.00  0.00           H  
HETATM   50  H23 UNL     1      -0.499  -0.896   0.846  1.00  0.00           H  
HETATM   51  H24 UNL     1      -2.295  -2.999  -0.476  1.00  0.00           H  
HETATM   52  H25 UNL     1      -1.838  -1.503  -1.279  1.00  0.00           H  
HETATM   53  H26 UNL     1      -3.692  -1.700   1.190  1.00  0.00           H  
HETATM   54  H27 UNL     1      -4.675  -2.270  -0.662  1.00  0.00           H  
HETATM   55  H28 UNL     1      -4.050   0.626   1.000  1.00  0.00           H  
HETATM   56  H29 UNL     1      -1.552   1.189   1.395  1.00  0.00           H  
HETATM   57  H30 UNL     1      -1.778   0.516  -1.064  1.00  0.00           H  
HETATM   58  H31 UNL     1      -3.491   0.734  -1.507  1.00  0.00           H  
HETATM   59  H32 UNL     1      -2.381   2.807  -1.596  1.00  0.00           H  
HETATM   60  H33 UNL     1      -1.677   2.690   0.025  1.00  0.00           H  
HETATM   61  H34 UNL     1      -4.613   3.015  -0.782  1.00  0.00           H  
HETATM   62  H35 UNL     1      -4.102   2.751   0.951  1.00  0.00           H  
HETATM   63  H36 UNL     1      -5.375   5.122   0.724  1.00  0.00           H  
CONECT    1    2   28   29   30
CONECT    2    3   31   32
CONECT    3    4   33   34
CONECT    4    5   35   36
CONECT    5    6   37   38
CONECT    6    7    8   39
CONECT    7   40
CONECT    8    9    9   41
CONECT    9   10   42
CONECT   10   11   16   43
CONECT   11   12   13   44
CONECT   12   45
CONECT   13   14   46   47
CONECT   14   15   16   48
CONECT   15   49
CONECT   16   17   50
CONECT   17   18   51   52
CONECT   18   19   20   53
CONECT   19   54
CONECT   20   21   22   55
CONECT   21   56
CONECT   22   23   57   58
CONECT   23   24   59   60
CONECT   24   25   61   62
CONECT   25   26   26   27
CONECT   27   63
END
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SMILES for HMDB0012109 (5,6-Dihydroxyprostaglandin F1a)

CCCCC[C@H](O)\C=C\[C@H]1[C@H](O)C[C@H](O)[C@@H]1CC(O)C(O)CCCC(O)=O
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INCHI for HMDB0012109 (5,6-Dihydroxyprostaglandin F1a)

InChI=1S/C20H36O7/c1-2-3-4-6-13(21)9-10-14-15(18(24)12-17(14)23)11-19(25)16(22)7-5-8-20(26)27/h9-10,13-19,21-25H,2-8,11-12H2,1H3,(H,26,27)/b10-9+/t13-,14+,15+,16?,17+,18-,19?/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
5,6-Hydroxyprostaglandin F1alphaHMDB
ProstaglandinsHMDB
5,6-Dihydroxyprostaglandin F1MeSH, HMDB
5,6-DH-PGF1MeSH, HMDB
7-[(1R,2R,3R,5S)-3,5-Dihydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]cyclopentyl]-5,6-dihydroxyheptanoateGenerator, HMDB
Chemical FormulaC20H36O7
Average Molecular Weight388.4956
Monoisotopic Molecular Weight388.246103506
IUPAC Name7-[(1R,2R,3R,5S)-3,5-dihydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]cyclopentyl]-5,6-dihydroxyheptanoic acid
Traditional Name7-[(1R,2R,3R,5S)-3,5-dihydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]cyclopentyl]-5,6-dihydroxyheptanoic acid
CAS Registry Number11000-26-3
SMILES
CCCCC[C@H](O)\C=C\[C@H]1[C@H](O)C[C@H](O)[C@@H]1CC(O)C(O)CCCC(O)=O
InChI Identifier
InChI=1S/C20H36O7/c1-2-3-4-6-13(21)9-10-14-15(18(24)12-17(14)23)11-19(25)16(22)7-5-8-20(26)27/h9-10,13-19,21-25H,2-8,11-12H2,1H3,(H,26,27)/b10-9+/t13-,14+,15+,16?,17+,18-,19?/m0/s1
InChI KeySAAOVBGAFHJPIF-NYNACFBQSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassEicosanoids
Direct ParentProstaglandins and related compounds
Alternative Parents
Substituents
  • Prostaglandin skeleton
  • Long-chain fatty acid
  • Fatty alcohol
  • Hydroxy fatty acid
  • Cyclopentanol
  • Cyclic alcohol
  • Secondary alcohol
  • Monocarboxylic acid or derivatives
  • Carboxylic acid
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Organooxygen compound
  • Organic oxide
  • Alcohol
  • Organic oxygen compound
  • Carbonyl group
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic 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
Predicted Chromatographic Properties
Spectra
Biological Properties
Cellular Locations
  • Extracellular
  • Membrane
Biospecimen LocationsNot Available
Tissue LocationsNot Available
Pathways
Normal Concentrations
Not Available
Abnormal Concentrations
Not Available
Associated Disorders and Diseases
Disease ReferencesNone
Associated OMIM IDsNone
DrugBank IDNot Available
Phenol Explorer Compound IDNot Available
FooDB IDFDB028773
KNApSAcK IDNot Available
Chemspider ID4944203
KEGG Compound ID C06475
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound6439819
PDB IDNot Available
ChEBI ID139312
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. Gunstone, Frank D., John L. Harwood, and Albert J. Dijkstra (2007). The lipid handbook with CD-ROM. CRC Press.