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Showing metabocard for PI(18:1(9Z)/PGD1) (HMDB0276642)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-13 06:04:58 UTC
Update Date2022-11-30 20:00:50 UTC
HMDB IDHMDB0276642
Secondary Accession NumbersNone
Metabolite Identification
Common NamePI(18:1(9Z)/PGD1)
DescriptionPI(18:1(9Z)/PGD1) is an oxidized phosphatidylinositol (PI). Phosphatidylinositols are important lipids, both as a key membrane constituent and as a participant in essential metabolic processes, both directly and via a number of metabolites. Phosphatidylinositols are acidic (anionic) phospholipids that consist of a phosphatidic acid backbone, linked via the phosphate group to inositol (hexahydroxycyclohexane). Phosphatidylinositols can have many different combinations of fatty acids of varying lengths and saturation attached at the C-1 and C-2 positions. PI(18:1(9Z)/PGD1), in particular, consists of one chain of 9Z-octadecenoyl at the C-1 position and one chain of Prostaglandin D1 at the C-2 position. The inositol group that is part of every phosphatidylinositol lipid is covalently linked to the phosphate group that acts as a bridge to the lipid tail. In most organisms, the stereochemical form of this inositol is myo-D-inositol (with one axial hydroxyl in position 2 with the remainder equatorial), although other forms can be found in certain plant phosphatidylinositols. Phosphatidylinositol is especially abundant in brain tissue, where it can amount to 10% of the phospholipids, but it is present in all tissues and cell types. There is usually less of it than of phosphatidylcholine, phosphatidylethanolamine and phosphatidylserine. In animal tissues, phosphatidylinositol is the primary source of the arachidonic acid required for biosynthesis of eicosanoids, including prostaglandins, via the action of the enzyme phospholipase A2. Phosphatidylinositol can be phosphorylated by a number of different kinases that place the phosphate moiety on positions 4 and 5 of the inositol ring, although position 3 can also be phosphorylated by a specific kinase. Seven different isomers are known, but the most important in both quantitative and biological terms are phosphatidylinositol 4-phosphate and phosphatidylinositol 4,5-bisphosphate. Phosphatidylinositol and the phosphatidylinositol phosphates are the main source of diacylglycerols that serve as signaling molecules, via the action of phospholipase C enzymes. While most phospholipids have a saturated fatty acid on C-1 and an unsaturated fatty acid on C-2 of the glycerol backbone, the fatty acid distribution at the C-1 and C-2 positions of glycerol within phospholipids is continually in flux, owing to phospholipid degradation and the continuous phospholipid remodeling that occurs while these molecules are in membranes. PIs composed exclusively of non-phosphorylated inositol exhibit a net charge of -1 at physiological pH. Molecules with phosphorylated inositol (such as PIP, PIP2, PIP3, etc.) are termed polyphosphoinositides. The polyphosphoinositides are important intracellular transducers of signals emanating from the plasma membrane. The synthesis of PI involves CDP-activated 1,2-diacylglycerol condensation with myo-inositol.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0276642 (PI(18:1(9Z)/PGD1))


  Mrv1652309132108052D          

 64 65  0  0  1  0            999 V2000
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    1.9596   -0.1295    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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    6.1653    1.9704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 51 63  1  0  0  0  0
 63 64  1  6  0  0  0
M  END
Download

3D MOL for HMDB0276642 (PI(18:1(9Z)/PGD1))

HMDB0276642
     RDKit          3D
PI(18:1(9Z)/PGD1)
147148  0  0  0  0  0  0  0  0999 V2000
   12.6897   -1.4647    2.1143 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7680   -2.7385    1.3159 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8826   -2.6891    0.3222 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7450   -1.5722   -0.6735 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4702   -1.6967   -1.4630 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3583   -0.5783   -2.4710 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3635    0.7898   -1.8583 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1983    1.0164   -0.9263 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9179    0.9016   -1.6351 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0101    1.8991   -1.7447 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2595    3.2143   -1.1382 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3361    3.6923   -0.0953 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9410    3.9968   -0.3795 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0245    2.9585   -0.8880 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8718    1.7279   -0.0458 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3956    1.9783    1.3404 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0955    2.6793    1.4833 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9382    2.0081    0.8788 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7858    2.5095    1.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0572    0.8933    0.1005 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9874    0.2257   -0.4742 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0627   -0.4778    0.5320 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0969   -0.9798   -0.3589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8581   -1.8624    0.3551 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2965   -3.2264   -0.5334 P   0  0  0  0  0  5  0  0  0  0  0  0
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   -5.4600    1.6066   -0.0012 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -1.6918    2.2273    1.8342 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -0.2357    0.3672    2.5376 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.9318    1.2263    0.2252 C   0  0  1  0  0  0  0  0  0  0  0  0
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   -9.1287   -2.9612    0.5266 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2647   -3.8550    0.3191 C   0  0  1  0  0  0  0  0  0  0  0  0
  -10.7230   -4.3881    1.5532 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3568   -3.3570   -0.5093 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1905   -2.2123   -0.2365 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8364   -0.8121   -0.1875 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8484   -0.2217    0.7241 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8636    1.3432    0.5562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7495   -2.7991   -0.3228 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.5794   -3.2166   -1.6463 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5307   -2.1969    0.2801 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9841   -3.1616    1.1637 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.6024   -0.8397    1.8944 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7151   -1.6853    3.2131 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7583   -0.9247    1.8811 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.0059   -3.5644    2.0290 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7891   -2.9463    0.8249 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.8466   -2.5976    0.8839 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.8994   -3.6703   -0.2314 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.6430   -1.6375   -1.3452 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.7379   -0.6220   -0.1270 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.5693   -2.6427   -2.0639 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.5989   -1.7298   -0.8058 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.1721   -0.6683   -3.2187 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3911   -0.7080   -3.0382 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.3689    1.5465   -2.6917 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.2986    0.9756   -1.3064 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3631    1.8959   -0.3215 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2287    0.1464   -0.1880 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0276642 (PI(18:1(9Z)/PGD1))


  Mrv1652309132108052D          

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M  END
> <DATABASE_ID>
HMDB0276642

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H]1COP(O)(=O)O[C@H]2[C@H](O)[C@@H](O)[C@H](O)[C@@H](CCCCCCC(=O)O1)[C@@H](O)CC(=O)[C@H](\C=C\[C@@H](O)CCCCC)[C@@H](O)[C@H]2O

> <INCHI_IDENTIFIER>
InChI=1S/C47H83O16P/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-23-27-40(51)60-32-35-33-61-64(58,59)63-47-45(56)43(54)37(30-29-34(48)25-21-6-4-2)39(50)31-38(49)36(42(53)44(55)46(47)57)26-22-19-20-24-28-41(52)62-35/h12-13,29-30,34-38,42-49,53-57H,3-11,14-28,31-33H2,1-2H3,(H,58,59)/b13-12-,30-29+/t34-,35+,36-,37-,38-,42+,43+,44-,45+,46+,47+/m0/s1

> <INCHI_KEY>
NMAOXAJNACLASH-ZJYNYYDKSA-N

> <FORMULA>
C47H83O16P

> <MOLECULAR_WEIGHT>
935.139

> <EXACT_MASS>
934.541873591

> <JCHEM_ACCEPTOR_COUNT>
12

> <JCHEM_ATOM_COUNT>
147

> <JCHEM_AVERAGE_POLARIZABILITY>
103.67469606142902

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(1R,6R,15S,16S,19R,20R,21R,22R,23S,24R)-3,16,20,21,22,23,24-heptahydroxy-19-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3,8,18-trioxo-2,4,7-trioxa-3lambda5-phosphabicyclo[13.6.3]tetracosan-6-yl]methyl (9Z)-octadec-9-enoate

> <ALOGPS_LOGP>
4.14

> <JCHEM_LOGP>
6.737529846333334

> <ALOGPS_LOGS>
-4.86

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
9.183249467009922

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.833266277432383

> <JCHEM_PKA_STRONGEST_BASIC>
-2.937540246714592

> <JCHEM_POLAR_SURFACE_AREA>
267.03999999999996

> <JCHEM_REFRACTIVITY>
242.1765000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
24

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.28e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(1R,6R,15S,16S,19R,20R,21R,22R,23S,24R)-3,16,20,21,22,23,24-heptahydroxy-19-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3,8,18-trioxo-2,4,7-trioxa-3lambda5-phosphabicyclo[13.6.3]tetracosan-6-yl]methyl (9Z)-octadec-9-enoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0276642 (PI(18:1(9Z)/PGD1))

HMDB0276642
     RDKit          3D
PI(18:1(9Z)/PGD1)
147148  0  0  0  0  0  0  0  0999 V2000
   12.6897   -1.4647    2.1143 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7680   -2.7385    1.3159 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8826   -2.6891    0.3222 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7450   -1.5722   -0.6735 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4702   -1.6967   -1.4630 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3583   -0.5783   -2.4710 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3635    0.7898   -1.8583 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1983    1.0164   -0.9263 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9179    0.9016   -1.6351 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0101    1.8991   -1.7447 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2595    3.2143   -1.1382 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.3361    3.6923   -0.0953 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9410    3.9968   -0.3795 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.0245    2.9585   -0.8880 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8718    1.7279   -0.0458 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3956    1.9783    1.3404 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0955    2.6793    1.4833 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9382    2.0081    0.8788 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7858    2.5095    1.1072 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0572    0.8933    0.1005 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9874    0.2257   -0.4742 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0627   -0.4778    0.5320 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0969   -0.9798   -0.3589 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8581   -1.8624    0.3551 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2965   -3.2264   -0.5334 P   0  0  0  0  0  5  0  0  0  0  0  0
   -0.3144   -3.4132   -1.6828 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3330   -4.6082    0.4522 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8467   -2.9876   -1.1516 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4367   -1.8330   -0.6585 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.8134   -0.9356   -1.7970 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.9316   -1.2512   -2.8587 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6777    0.5393   -1.4258 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.9052    1.1440   -2.4204 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9946    1.2616   -1.3853 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.9497    2.4591   -2.1265 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.4600    1.6066   -0.0012 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.2976    3.0539    0.3622 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9444    3.6228    0.1844 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3171    4.1028    1.4762 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8796    2.9821    2.3833 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6918    2.2273    1.8342 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6799    0.8018    2.3801 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2357    0.3672    2.5376 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0809    0.0314    3.7310 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5788    0.3640    1.4746 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9318    1.2263    0.2252 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.5464    0.9147   -0.9792 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.1134    0.2480    1.3207 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9699   -1.1688    1.0391 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7981   -1.8896    2.0444 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9931   -1.8971   -0.2248 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.1665   -2.7903   -0.3843 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1287   -2.9612    0.5266 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2647   -3.8550    0.3191 C   0  0  1  0  0  0  0  0  0  0  0  0
  -10.7230   -4.3881    1.5532 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3568   -3.3570   -0.5093 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1905   -2.2123   -0.2365 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.8364   -0.8121   -0.1875 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8484   -0.2217    0.7241 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8636    1.3432    0.5562 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7495   -2.7991   -0.3228 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.5794   -3.2166   -1.6463 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5307   -2.1969    0.2801 C   0  0  1  0  0  0  0  0  0  0  0  0
   -3.9841   -3.1616    1.1637 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.6024   -0.8397    1.8944 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7151   -1.6853    3.2131 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7583   -0.9247    1.8811 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.0059   -3.5644    2.0290 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7891   -2.9463    0.8249 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.8466   -2.5976    0.8839 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.8994   -3.6703   -0.2314 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.6430   -1.6375   -1.3452 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.7379   -0.6220   -0.1270 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.5693   -2.6427   -2.0639 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.5989   -1.7298   -0.8058 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.1721   -0.6683   -3.2187 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3911   -0.7080   -3.0382 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.3689    1.5465   -2.6917 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.2986    0.9756   -1.3064 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3631    1.8959   -0.3215 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2287    0.1464   -0.1880 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6885   -0.0687   -2.1064 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1461    1.6326   -2.3087 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1435    3.9824   -2.0123 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3404    3.3968   -0.8780 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8004    4.6575    0.3215 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.3877    2.9354    0.7569 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.4597    4.5762    0.4839 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.9489    4.8095   -1.1943 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2636    2.6860   -1.9239 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9845    3.4486   -1.0045 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8889    1.2435    0.0503 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2494    1.0031   -0.5921 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1890    2.4815    1.9392 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2860    0.9704    1.8339 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2016    3.7409    1.0924 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.8480    2.8605    2.5743 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4011    0.9650   -1.0715 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3504   -0.5138   -1.2152 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6326   -1.3871    0.8738 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3323   -1.4004   -1.2927 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6680   -0.0754   -0.6114 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9154   -5.2949    0.0329 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6577   -1.2863   -0.0714 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8161   -1.0628   -2.1990 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2002   -0.5967   -2.9351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1609    0.5660   -0.4428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5056    1.4741   -3.1203 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7756    0.6385   -1.8647 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.6206    2.4768   -2.8400 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8890    1.0095    0.7428 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1002    3.6500   -0.1425 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5501    3.1254    1.4552 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.2164    3.0173   -0.3484 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0652    4.5656   -0.4339 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9848    4.8231    2.0008 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4128    4.6822    1.2000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6741    2.2435    2.5998 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5266    3.4803    3.3274 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7579    2.1389    0.7358 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7516    2.7608    2.1166 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1157    0.8673    3.3900 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2706    0.1050    1.7935 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4826    2.1680    0.5483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4731    1.2117   -1.0623 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.0597   -3.7383    0.2260 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.8357   -1.3700    0.9527 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1806   -2.7264    1.5343 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
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 33108  1  0
 34109  1  6
 35110  1  0
 36111  1  1
 37112  1  0
 37113  1  0
 38114  1  0
 38115  1  0
 39116  1  0
 39117  1  0
 40118  1  0
 40119  1  0
 41120  1  0
 41121  1  0
 42122  1  0
 42123  1  0
 46124  1  1
 47125  1  0
 48126  1  0
 48127  1  0
 51128  1  6
 52129  1  0
 53130  1  0
 54131  1  6
 55132  1  0
 56133  1  0
 56134  1  0
 57135  1  0
 57136  1  0
 58137  1  0
 58138  1  0
 59139  1  0
 59140  1  0
 60141  1  0
 60142  1  0
 60143  1  0
 61144  1  1
 62145  1  0
 63146  1  1
 64147  1  0
M  END
Download

PDB for HMDB0276642 (PI(18:1(9Z)/PGD1))

HEADER    PROTEIN                                 13-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-SEP-21         0                                  
HETATM    1  O   UNK     0       0.777  -5.361   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.733  -4.067   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.933  -2.707   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.629  -3.082   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       0.970  -1.115   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -0.470  -0.395   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       2.104   0.005   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       3.658  -0.242   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0       4.864   1.014   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0       4.714   2.730   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.518   1.936   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       6.172   1.929   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       7.753   2.072   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.670   1.381   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      10.022   2.895   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      11.509   3.678   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0      13.144   3.757   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0      13.437   5.310   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0      14.571   2.983   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      16.023   3.620   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      17.339   2.716   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      18.516   3.775   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      19.930   3.054   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      21.103   4.129   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      22.632   3.678   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      23.768   4.801   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      25.306   4.468   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      25.778   3.002   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      27.283   2.677   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      27.754   1.211   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      26.720   0.070   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      27.191  -1.396   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      26.157  -2.537   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      26.628  -4.004   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      25.594  -5.145   0.000  0.00  0.00           C+0
HETATM   36  O   UNK     0       9.343  -0.031   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      10.950  -1.193   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      12.904  -1.104   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      11.402  -2.686   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      10.570  -3.997   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0       9.015  -3.885   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0       7.831  -4.897   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0       6.340  -4.414   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0       4.618  -4.022   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0       3.174  -4.727   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0       4.084  -6.008   0.000  0.00  0.00           C+0
HETATM   47  O   UNK     0       3.632  -7.594   0.000  0.00  0.00           O+0
HETATM   48  C   UNK     0       5.281  -4.987   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0       5.709  -3.261   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0       7.373  -3.990   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0       5.783  -1.668   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0       7.324  -0.880   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0       9.175  -0.996   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      10.491   0.116   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0      10.569   1.655   0.000  0.00  0.00           O+0
HETATM   56  C   UNK     0      12.037  -0.058   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      12.147  -1.775   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      13.647  -2.448   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      14.754  -3.699   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      16.263  -3.392   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       3.483   0.801   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0       2.522   2.412   0.000  0.00  0.00           O+0
HETATM   63  C   UNK     0       4.824  -0.381   0.000  0.00  0.00           C+0
HETATM   64  O   UNK     0       6.255  -0.495   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   45                                                  
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8   61                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15   36                                                  
CONECT   15   14   16                                                       
CONECT   16   15   17                                                       
CONECT   17   16   18   19                                                  
CONECT   18   17                                                            
CONECT   19   17   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22                                                       
CONECT   22   21   23                                                       
CONECT   23   22   24                                                       
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   27                                                       
CONECT   27   26   28                                                       
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31                                                       
CONECT   31   30   32                                                       
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34                                                            
CONECT   36   14   37                                                       
CONECT   37   36   38   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44    2   46                                                  
CONECT   46   45   47   48                                                  
CONECT   47   46                                                            
CONECT   48   46   49                                                       
CONECT   49   48   50   51                                                  
CONECT   50   49                                                            
CONECT   51   49   52   63                                                  
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55   56                                                  
CONECT   55   54                                                            
CONECT   56   54   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59                                                            
CONECT   61    7   62   63                                                  
CONECT   62   61                                                            
CONECT   63   61   51   64                                                  
CONECT   64   63                                                            
MASTER        0    0    0    0    0    0    0    0   64    0  130    0
END
Download

3D PDB for HMDB0276642 (PI(18:1(9Z)/PGD1))

COMPND    HMDB0276642
HETATM    1  C1  UNL     1      12.690  -1.465   2.114  1.00  0.00           C  
HETATM    2  C2  UNL     1      12.768  -2.739   1.316  1.00  0.00           C  
HETATM    3  C3  UNL     1      13.883  -2.689   0.322  1.00  0.00           C  
HETATM    4  C4  UNL     1      13.745  -1.572  -0.674  1.00  0.00           C  
HETATM    5  C5  UNL     1      12.470  -1.697  -1.463  1.00  0.00           C  
HETATM    6  C6  UNL     1      12.358  -0.578  -2.471  1.00  0.00           C  
HETATM    7  C7  UNL     1      12.364   0.790  -1.858  1.00  0.00           C  
HETATM    8  C8  UNL     1      11.198   1.016  -0.926  1.00  0.00           C  
HETATM    9  C9  UNL     1       9.918   0.902  -1.635  1.00  0.00           C  
HETATM   10  C10 UNL     1       9.010   1.899  -1.745  1.00  0.00           C  
HETATM   11  C11 UNL     1       9.259   3.214  -1.138  1.00  0.00           C  
HETATM   12  C12 UNL     1       8.336   3.692  -0.095  1.00  0.00           C  
HETATM   13  C13 UNL     1       6.941   3.997  -0.379  1.00  0.00           C  
HETATM   14  C14 UNL     1       6.025   2.958  -0.888  1.00  0.00           C  
HETATM   15  C15 UNL     1       5.872   1.728  -0.046  1.00  0.00           C  
HETATM   16  C16 UNL     1       5.396   1.978   1.340  1.00  0.00           C  
HETATM   17  C17 UNL     1       4.096   2.679   1.483  1.00  0.00           C  
HETATM   18  C18 UNL     1       2.938   2.008   0.879  1.00  0.00           C  
HETATM   19  O1  UNL     1       1.786   2.510   1.107  1.00  0.00           O  
HETATM   20  O2  UNL     1       3.057   0.893   0.100  1.00  0.00           O  
HETATM   21  C19 UNL     1       1.987   0.226  -0.474  1.00  0.00           C  
HETATM   22  C20 UNL     1       1.063  -0.478   0.532  1.00  0.00           C  
HETATM   23  C21 UNL     1      -0.097  -0.980  -0.359  1.00  0.00           C  
HETATM   24  O3  UNL     1      -0.858  -1.862   0.355  1.00  0.00           O  
HETATM   25  P1  UNL     1      -1.297  -3.226  -0.533  1.00  0.00           P  
HETATM   26  O4  UNL     1      -0.314  -3.413  -1.683  1.00  0.00           O  
HETATM   27  O5  UNL     1      -1.333  -4.608   0.452  1.00  0.00           O  
HETATM   28  O6  UNL     1      -2.847  -2.988  -1.152  1.00  0.00           O  
HETATM   29  C22 UNL     1      -3.437  -1.833  -0.659  1.00  0.00           C  
HETATM   30  C23 UNL     1      -3.813  -0.936  -1.797  1.00  0.00           C  
HETATM   31  O7  UNL     1      -2.932  -1.251  -2.859  1.00  0.00           O  
HETATM   32  C24 UNL     1      -3.678   0.539  -1.426  1.00  0.00           C  
HETATM   33  O8  UNL     1      -2.905   1.144  -2.420  1.00  0.00           O  
HETATM   34  C25 UNL     1      -4.995   1.262  -1.385  1.00  0.00           C  
HETATM   35  O9  UNL     1      -4.950   2.459  -2.126  1.00  0.00           O  
HETATM   36  C26 UNL     1      -5.460   1.607  -0.001  1.00  0.00           C  
HETATM   37  C27 UNL     1      -5.298   3.054   0.362  1.00  0.00           C  
HETATM   38  C28 UNL     1      -3.944   3.623   0.184  1.00  0.00           C  
HETATM   39  C29 UNL     1      -3.317   4.103   1.476  1.00  0.00           C  
HETATM   40  C30 UNL     1      -2.880   2.982   2.383  1.00  0.00           C  
HETATM   41  C31 UNL     1      -1.692   2.227   1.834  1.00  0.00           C  
HETATM   42  C32 UNL     1      -1.680   0.802   2.380  1.00  0.00           C  
HETATM   43  C33 UNL     1      -0.236   0.367   2.538  1.00  0.00           C  
HETATM   44  O10 UNL     1       0.081   0.031   3.731  1.00  0.00           O  
HETATM   45  O11 UNL     1       0.579   0.364   1.475  1.00  0.00           O  
HETATM   46  C34 UNL     1      -6.932   1.226   0.225  1.00  0.00           C  
HETATM   47  O12 UNL     1      -7.546   0.915  -0.979  1.00  0.00           O  
HETATM   48  C35 UNL     1      -7.113   0.248   1.321  1.00  0.00           C  
HETATM   49  C36 UNL     1      -6.970  -1.169   1.039  1.00  0.00           C  
HETATM   50  O13 UNL     1      -6.798  -1.890   2.044  1.00  0.00           O  
HETATM   51  C37 UNL     1      -6.993  -1.897  -0.225  1.00  0.00           C  
HETATM   52  C38 UNL     1      -8.166  -2.790  -0.384  1.00  0.00           C  
HETATM   53  C39 UNL     1      -9.129  -2.961   0.527  1.00  0.00           C  
HETATM   54  C40 UNL     1     -10.265  -3.855   0.319  1.00  0.00           C  
HETATM   55  O14 UNL     1     -10.723  -4.388   1.553  1.00  0.00           O  
HETATM   56  C41 UNL     1     -11.357  -3.357  -0.509  1.00  0.00           C  
HETATM   57  C42 UNL     1     -12.191  -2.212  -0.237  1.00  0.00           C  
HETATM   58  C43 UNL     1     -11.836  -0.812  -0.188  1.00  0.00           C  
HETATM   59  C44 UNL     1     -10.848  -0.222   0.724  1.00  0.00           C  
HETATM   60  C45 UNL     1     -10.864   1.343   0.556  1.00  0.00           C  
HETATM   61  C46 UNL     1      -5.750  -2.799  -0.323  1.00  0.00           C  
HETATM   62  O15 UNL     1      -5.579  -3.217  -1.646  1.00  0.00           O  
HETATM   63  C47 UNL     1      -4.531  -2.197   0.280  1.00  0.00           C  
HETATM   64  O16 UNL     1      -3.984  -3.162   1.164  1.00  0.00           O  
HETATM   65  H1  UNL     1      13.602  -0.840   1.894  1.00  0.00           H  
HETATM   66  H2  UNL     1      12.715  -1.685   3.213  1.00  0.00           H  
HETATM   67  H3  UNL     1      11.758  -0.925   1.881  1.00  0.00           H  
HETATM   68  H4  UNL     1      13.006  -3.564   2.029  1.00  0.00           H  
HETATM   69  H5  UNL     1      11.789  -2.946   0.825  1.00  0.00           H  
HETATM   70  H6  UNL     1      14.847  -2.598   0.884  1.00  0.00           H  
HETATM   71  H7  UNL     1      13.899  -3.670  -0.231  1.00  0.00           H  
HETATM   72  H8  UNL     1      14.643  -1.638  -1.345  1.00  0.00           H  
HETATM   73  H9  UNL     1      13.738  -0.622  -0.127  1.00  0.00           H  
HETATM   74  H10 UNL     1      12.569  -2.643  -2.064  1.00  0.00           H  
HETATM   75  H11 UNL     1      11.599  -1.730  -0.806  1.00  0.00           H  
HETATM   76  H12 UNL     1      13.172  -0.668  -3.219  1.00  0.00           H  
HETATM   77  H13 UNL     1      11.391  -0.708  -3.038  1.00  0.00           H  
HETATM   78  H14 UNL     1      12.369   1.547  -2.692  1.00  0.00           H  
HETATM   79  H15 UNL     1      13.299   0.976  -1.306  1.00  0.00           H  
HETATM   80  H16 UNL     1      11.363   1.896  -0.322  1.00  0.00           H  
HETATM   81  H17 UNL     1      11.229   0.146  -0.188  1.00  0.00           H  
HETATM   82  H18 UNL     1       9.688  -0.069  -2.106  1.00  0.00           H  
HETATM   83  H19 UNL     1       8.146   1.633  -2.309  1.00  0.00           H  
HETATM   84  H20 UNL     1       9.143   3.982  -2.012  1.00  0.00           H  
HETATM   85  H21 UNL     1      10.340   3.397  -0.878  1.00  0.00           H  
HETATM   86  H22 UNL     1       8.800   4.657   0.321  1.00  0.00           H  
HETATM   87  H23 UNL     1       8.388   2.935   0.757  1.00  0.00           H  
HETATM   88  H24 UNL     1       6.460   4.576   0.484  1.00  0.00           H  
HETATM   89  H25 UNL     1       6.949   4.810  -1.194  1.00  0.00           H  
HETATM   90  H26 UNL     1       6.264   2.686  -1.924  1.00  0.00           H  
HETATM   91  H27 UNL     1       4.985   3.449  -1.004  1.00  0.00           H  
HETATM   92  H28 UNL     1       6.889   1.243   0.050  1.00  0.00           H  
HETATM   93  H29 UNL     1       5.249   1.003  -0.592  1.00  0.00           H  
HETATM   94  H30 UNL     1       6.189   2.482   1.939  1.00  0.00           H  
HETATM   95  H31 UNL     1       5.286   0.970   1.834  1.00  0.00           H  
HETATM   96  H32 UNL     1       4.202   3.741   1.092  1.00  0.00           H  
HETATM   97  H33 UNL     1       3.848   2.861   2.574  1.00  0.00           H  
HETATM   98  H34 UNL     1       1.401   0.965  -1.071  1.00  0.00           H  
HETATM   99  H35 UNL     1       2.350  -0.514  -1.215  1.00  0.00           H  
HETATM  100  H36 UNL     1       1.633  -1.387   0.874  1.00  0.00           H  
HETATM  101  H37 UNL     1       0.332  -1.400  -1.293  1.00  0.00           H  
HETATM  102  H38 UNL     1      -0.668  -0.075  -0.611  1.00  0.00           H  
HETATM  103  H39 UNL     1      -1.915  -5.295   0.033  1.00  0.00           H  
HETATM  104  H40 UNL     1      -2.658  -1.286  -0.071  1.00  0.00           H  
HETATM  105  H41 UNL     1      -4.816  -1.063  -2.199  1.00  0.00           H  
HETATM  106  H42 UNL     1      -2.200  -0.597  -2.935  1.00  0.00           H  
HETATM  107  H43 UNL     1      -3.161   0.566  -0.443  1.00  0.00           H  
HETATM  108  H44 UNL     1      -3.506   1.474  -3.120  1.00  0.00           H  
HETATM  109  H45 UNL     1      -5.776   0.638  -1.865  1.00  0.00           H  
HETATM  110  H46 UNL     1      -5.621   2.477  -2.840  1.00  0.00           H  
HETATM  111  H47 UNL     1      -4.889   1.009   0.743  1.00  0.00           H  
HETATM  112  H48 UNL     1      -6.100   3.650  -0.142  1.00  0.00           H  
HETATM  113  H49 UNL     1      -5.550   3.125   1.455  1.00  0.00           H  
HETATM  114  H50 UNL     1      -3.216   3.017  -0.348  1.00  0.00           H  
HETATM  115  H51 UNL     1      -4.065   4.566  -0.434  1.00  0.00           H  
HETATM  116  H52 UNL     1      -3.985   4.823   2.001  1.00  0.00           H  
HETATM  117  H53 UNL     1      -2.413   4.682   1.200  1.00  0.00           H  
HETATM  118  H54 UNL     1      -3.674   2.244   2.600  1.00  0.00           H  
HETATM  119  H55 UNL     1      -2.527   3.480   3.327  1.00  0.00           H  
HETATM  120  H56 UNL     1      -1.758   2.139   0.736  1.00  0.00           H  
HETATM  121  H57 UNL     1      -0.752   2.761   2.117  1.00  0.00           H  
HETATM  122  H58 UNL     1      -2.116   0.867   3.390  1.00  0.00           H  
HETATM  123  H59 UNL     1      -2.271   0.105   1.794  1.00  0.00           H  
HETATM  124  H60 UNL     1      -7.483   2.168   0.548  1.00  0.00           H  
HETATM  125  H61 UNL     1      -8.473   1.212  -1.062  1.00  0.00           H  
HETATM  126  H62 UNL     1      -8.074   0.495   1.863  1.00  0.00           H  
HETATM  127  H63 UNL     1      -6.333   0.522   2.098  1.00  0.00           H  
HETATM  128  H64 UNL     1      -6.951  -1.287  -1.143  1.00  0.00           H  
HETATM  129  H65 UNL     1      -8.269  -3.353  -1.302  1.00  0.00           H  
HETATM  130  H66 UNL     1      -8.985  -2.384   1.440  1.00  0.00           H  
HETATM  131  H67 UNL     1      -9.838  -4.784  -0.199  1.00  0.00           H  
HETATM  132  H68 UNL     1     -11.627  -4.736   1.343  1.00  0.00           H  
HETATM  133  H69 UNL     1     -12.040  -4.269  -0.789  1.00  0.00           H  
HETATM  134  H70 UNL     1     -10.939  -3.179  -1.591  1.00  0.00           H  
HETATM  135  H71 UNL     1     -13.050  -2.261  -1.048  1.00  0.00           H  
HETATM  136  H72 UNL     1     -12.814  -2.504   0.713  1.00  0.00           H  
HETATM  137  H73 UNL     1     -11.565  -0.464  -1.255  1.00  0.00           H  
HETATM  138  H74 UNL     1     -12.832  -0.224  -0.034  1.00  0.00           H  
HETATM  139  H75 UNL     1     -10.911  -0.402   1.778  1.00  0.00           H  
HETATM  140  H76 UNL     1      -9.794  -0.460   0.377  1.00  0.00           H  
HETATM  141  H77 UNL     1     -10.764   1.604  -0.496  1.00  0.00           H  
HETATM  142  H78 UNL     1     -11.828   1.638   1.023  1.00  0.00           H  
HETATM  143  H79 UNL     1     -10.051   1.690   1.220  1.00  0.00           H  
HETATM  144  H80 UNL     1      -6.060  -3.738   0.226  1.00  0.00           H  
HETATM  145  H81 UNL     1      -5.484  -4.204  -1.730  1.00  0.00           H  
HETATM  146  H82 UNL     1      -4.836  -1.370   0.953  1.00  0.00           H  
HETATM  147  H83 UNL     1      -3.181  -2.726   1.534  1.00  0.00           H  
CONECT    1    2   65   66   67
CONECT    2    3   68   69
CONECT    3    4   70   71
CONECT    4    5   72   73
CONECT    5    6   74   75
CONECT    6    7   76   77
CONECT    7    8   78   79
CONECT    8    9   80   81
CONECT    9   10   10   82
CONECT   10   11   83
CONECT   11   12   84   85
CONECT   12   13   86   87
CONECT   13   14   88   89
CONECT   14   15   90   91
CONECT   15   16   92   93
CONECT   16   17   94   95
CONECT   17   18   96   97
CONECT   18   19   19   20
CONECT   20   21
CONECT   21   22   98   99
CONECT   22   23   45  100
CONECT   23   24  101  102
CONECT   24   25
CONECT   25   26   26   27   28
CONECT   27  103
CONECT   28   29
CONECT   29   30   63  104
CONECT   30   31   32  105
CONECT   31  106
CONECT   32   33   34  107
CONECT   33  108
CONECT   34   35   36  109
CONECT   35  110
CONECT   36   37   46  111
CONECT   37   38  112  113
CONECT   38   39  114  115
CONECT   39   40  116  117
CONECT   40   41  118  119
CONECT   41   42  120  121
CONECT   42   43  122  123
CONECT   43   44   44   45
CONECT   46   47   48  124
CONECT   47  125
CONECT   48   49  126  127
CONECT   49   50   50   51
CONECT   51   52   61  128
CONECT   52   53   53  129
CONECT   53   54  130
CONECT   54   55   56  131
CONECT   55  132
CONECT   56   57  133  134
CONECT   57   58  135  136
CONECT   58   59  137  138
CONECT   59   60  139  140
CONECT   60  141  142  143
CONECT   61   62   63  144
CONECT   62  145
CONECT   63   64  146
CONECT   64  147
END
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SMILES for HMDB0276642 (PI(18:1(9Z)/PGD1))

CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H]1COP(O)(=O)O[C@H]2[C@H](O)[C@@H](O)[C@H](O)[C@@H](CCCCCCC(=O)O1)[C@@H](O)CC(=O)[C@H](\C=C\[C@@H](O)CCCCC)[C@@H](O)[C@H]2O
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INCHI for HMDB0276642 (PI(18:1(9Z)/PGD1))

InChI=1S/C47H83O16P/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-23-27-40(51)60-32-35-33-61-64(58,59)63-47-45(56)43(54)37(30-29-34(48)25-21-6-4-2)39(50)31-38(49)36(42(53)44(55)46(47)57)26-22-19-20-24-28-41(52)62-35/h12-13,29-30,34-38,42-49,53-57H,3-11,14-28,31-33H2,1-2H3,(H,58,59)/b13-12-,30-29+/t34-,35+,36-,37-,38-,42+,43+,44-,45+,46+,47+/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[(1R,6R,15S,16S,19R,20R,21R,22R,23S,24R)-3,16,20,21,22,23,24-Heptahydroxy-19-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3,8,18-trioxo-2,4,7-trioxa-3-phosphabicyclo[13.6.3]tetracosan-6-yl]methyl (9Z)-octadec-9-enoic acidHMDB
Chemical FormulaC47H83O16P
Average Molecular Weight935.139
Monoisotopic Molecular Weight934.541873591
IUPAC Name[(1R,6R,15S,16S,19R,20R,21R,22R,23S,24R)-3,16,20,21,22,23,24-heptahydroxy-19-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3,8,18-trioxo-2,4,7-trioxa-3lambda5-phosphabicyclo[13.6.3]tetracosan-6-yl]methyl (9Z)-octadec-9-enoate
Traditional Name[(1R,6R,15S,16S,19R,20R,21R,22R,23S,24R)-3,16,20,21,22,23,24-heptahydroxy-19-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3,8,18-trioxo-2,4,7-trioxa-3lambda5-phosphabicyclo[13.6.3]tetracosan-6-yl]methyl (9Z)-octadec-9-enoate
CAS Registry NumberNot Available
SMILES
CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H]1COP(O)(=O)O[C@H]2[C@H](O)[C@@H](O)[C@H](O)[C@@H](CCCCCCC(=O)O1)[C@@H](O)CC(=O)[C@H](\C=C\[C@@H](O)CCCCC)[C@@H](O)[C@H]2O
InChI Identifier
InChI=1S/C47H83O16P/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-23-27-40(51)60-32-35-33-61-64(58,59)63-47-45(56)43(54)37(30-29-34(48)25-21-6-4-2)39(50)31-38(49)36(42(53)44(55)46(47)57)26-22-19-20-24-28-41(52)62-35/h12-13,29-30,34-38,42-49,53-57H,3-11,14-28,31-33H2,1-2H3,(H,58,59)/b13-12-,30-29+/t34-,35+,36-,37-,38-,42+,43+,44-,45+,46+,47+/m0/s1
InChI KeyNMAOXAJNACLASH-ZJYNYYDKSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as glycerophospholipids. These are derivatives of glycerophosphoric acid that contains at least one O-acyl, or O-alkyl, or O-(1-alkenyl) group attached to the glycerol residue.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassGlycerophospholipids
Sub ClassNot Available
Direct ParentGlycerophospholipids
Alternative Parents
Substituents
  • Glycerophospholipid
  • Fatty acid ester
  • Fatty acyl
  • Organic phosphoric acid derivative
  • Dicarboxylic acid or derivatives
  • Cyclic ketone
  • Secondary alcohol
  • Lactone
  • Ketone
  • Carboxylic acid ester
  • Oxacycle
  • Organoheterocyclic compound
  • Polyol
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic heteropolycyclic compound
Molecular FrameworkAliphatic heteropolycyclic compounds
External DescriptorsNot Available
Ontology
Physiological effect
Health effect
Disposition
Biological locationSource
Process
Naturally occurring process
RoleNot Available
Physical Properties
StateNot Available
Experimental Molecular Properties
PropertyValueReference
Melting PointNot AvailableNot Available
Boiling PointNot AvailableNot Available
Water SolubilityNot AvailableNot Available
LogPNot AvailableNot Available
Experimental Chromatographic PropertiesNot Available
Predicted Molecular Properties
PropertyValueSource
logP4.14ALOGPS
logP6.74ChemAxon
logS-4.9ALOGPS
pKa (Strongest Acidic)1.83ChemAxon
pKa (Strongest Basic)-2.9ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count12ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area267.04 ŲChemAxon
Rotatable Bond Count24ChemAxon
Refractivity242.18 m³·mol⁻¹ChemAxon
Polarizability103.67 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+301.67732859911
AllCCS[M+H-H2O]+302.04932859911
AllCCS[M+Na]+301.18132859911
AllCCS[M+NH4]+301.29732859911
AllCCS[M-H]-301.49532859911
AllCCS[M+Na-2H]-307.67332859911
AllCCS[M+HCOO]-314.45332859911
DeepCCS[M+H]+326.46930932474
DeepCCS[M-H]-324.74530932474
DeepCCS[M-2H]-359.39430932474
DeepCCS[M+Na]+333.04130932474

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, 2022.8.26 minutes32390414
Predicted by Siyang on May 30, 202219.9175 minutes33406817
Predicted by Siyang using ReTip algorithm on June 8, 20222.96 minutes32390414
Fem_Long = Waters ACQUITY UPLC HSS T3 C18 with Water:MeOH and 0.1% Formic Acid4690.2 seconds40023050
Fem_Lipids = Ascentis Express C18 with (60:40 water:ACN):(90:10 IPA:ACN) and 10mM NH4COOH + 0.1% Formic Acid145.9 seconds40023050
Life_Old = Waters ACQUITY UPLC BEH C18 with Water:(20:80 acetone:ACN) and 0.1% Formic Acid295.9 seconds40023050
Life_New = RP Waters ACQUITY UPLC HSS T3 C18 with Water:(30:70 MeOH:ACN) and 0.1% Formic Acid198.4 seconds40023050
RIKEN = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid589.5 seconds40023050
Eawag_XBridgeC18 = XBridge C18 3.5u 2.1x50 mm with Water:MeOH and 0.1% Formic Acid1030.8 seconds40023050
BfG_NTS_RP1 =Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) with Water:ACN and 0.1% Formic Acid903.9 seconds40023050
HILIC_BDD_2 = Merck SeQuant ZIC-HILIC with ACN(0.1% formic acid):water(16 mM ammonium formate)587.4 seconds40023050
UniToyama_Atlantis = RP Waters Atlantis T3 (2.1 x 150 mm, 5 um) with ACN:Water and 0.1% Formic Acid1973.7 seconds40023050
BDD_C18 = Hypersil Gold 1.9µm C18 with Water:ACN and 0.1% Formic Acid981.7 seconds40023050
UFZ_Phenomenex = Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex with Water:MeOH and 0.1% Formic Acid2206.5 seconds40023050
SNU_RIKEN_POS = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid623.4 seconds40023050
RPMMFDA = Waters ACQUITY UPLC BEH C18 with Water:ACN and 0.1% Formic Acid609.2 seconds40023050
MTBLS87 = Merck SeQuant ZIC-pHILIC column with ACN:Water and :ammonium carbonate216.9 seconds40023050
KI_GIAR_zic_HILIC_pH2_7 = Merck SeQuant ZIC-HILIC with ACN:Water and 0.1% FA74.8 seconds40023050
Meister zic-pHILIC pH9.3 = Merck SeQuant ZIC-pHILIC column with ACN:Water 5mM NH4Ac pH9.3 and 5mM ammonium acetate in water9.7 seconds40023050

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PI(18:1(9Z)/PGD1) 10V, Positive-QTOFsplash10-00kr-0000000009-8d2f1d5eca12293da8cd2021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PI(18:1(9Z)/PGD1) 20V, Positive-QTOFsplash10-014i-3100000189-f7f7f6794b7fb198de182021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PI(18:1(9Z)/PGD1) 40V, Positive-QTOFsplash10-0h90-7800009000-dfbedc79ff902296f19e2021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PI(18:1(9Z)/PGD1) 10V, Negative-QTOFsplash10-001i-0000000009-7e0603c73ca3ad95b38c2021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PI(18:1(9Z)/PGD1) 20V, Negative-QTOFsplash10-001i-0010002009-ef49bdb0e9afdbb476822021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PI(18:1(9Z)/PGD1) 40V, Negative-QTOFsplash10-0uk9-0000009010-21f882b347df74b7da022021-10-19Wishart LabView Spectrum
Biological Properties
Cellular LocationsNot Available
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 IDNot Available
KNApSAcK IDNot Available
Chemspider IDNot Available
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound156979994
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available