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Showing metabocard for PIP(PGD1/18:0) (HMDB0278821)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-13 10:53:47 UTC
Update Date2022-11-30 20:01:55 UTC
HMDB IDHMDB0278821
Secondary Accession NumbersNone
Metabolite Identification
Common NamePIP(PGD1/18:0)
DescriptionPIP(PGD1/18:0) is an oxidized phosphatidylinositol phosphate (PIP). As other PIPs, oxidized phosphatidylinositol phosphates are acidic (anionic) phospholipids that consist of a phosphatidic acid backbone, linked via the phosphate group to a phosphorylated inositol (hexahydroxycyclohexane). Phosphatidylinositol phosphates are generated from phosphatidylinositols, which are 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. Phosphatidylinositol phosphates can have many different combinations of fatty acids of varying lengths and saturation attached at the C-1 and C-2 positions. PIP(PGD1/18:0), in particular, consists of one chain of Prostaglandin D1 at the C-1 position and one chain of octadecanoyl at the C-2 position. The most important phosphatidylinositol phosphate in both quantitative and biological terms is phosphatidylinositol 4-phosphate. Phosphatidylinositol and the phosphatidylinositol phosphates are the main source of diacylglycerols that serve as signaling molecules, via the action of phospholipase C enzymes. Phosphatidylinositol phosphates are usually present at low levels only in tissues, typically at about 1 to 3% of the concentration of phosphatidylinositol.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0278821 (PIP(PGD1/18:0))


  Mrv1652309132112542D          

 68 69  0  0  1  0            999 V2000
    1.6643    6.1810    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9296    6.0011    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
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    0.6952    7.4842    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0314    6.7548    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.9717    7.6276    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.2639    5.9632    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.7878    5.5237    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7644    4.6990    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.6151    5.3108    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8650    4.8036    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4669    4.2664    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
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 61 67  1  0  0  0  0
 31 67  1  0  0  0  0
 67 68  1  6  0  0  0
M  END
Download

3D MOL for HMDB0278821 (PIP(PGD1/18:0))

HMDB0278821
     RDKit          3D
PIP(PGD1/18:0)
154155  0  0  0  0  0  0  0  0999 V2000
   18.3520   -2.4352    0.6682 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8986   -2.0079    0.2972 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8548   -1.5017   -1.0814 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5736   -1.1508   -1.6630 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6706   -0.1239   -1.1083 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0548   -0.3761    0.2214 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1380    0.7760    0.6398 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9992    0.9885   -0.3145 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1748    2.1480    0.2368 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9978    2.4454   -0.6598 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0492    1.2946   -0.8161 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4720    0.9005    0.5427 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5240   -0.2557    0.3553 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9029   -0.6971    1.6586 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1105    0.4203    2.3061 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9897    0.8951    1.4065 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0142   -0.1885    1.0820 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9627    0.3550    0.1941 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3085    0.4725   -1.0327 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6933    0.7231    0.5969 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846    1.2271   -0.3570 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3421    2.6185   -0.1308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8943    2.8064    0.4738 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4713    4.0325    0.7112 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1023    4.2050    1.7849 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3891    5.1689   -0.2365 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5377    5.1511   -1.2565 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.4434   -4.8989    0.9527 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0216   -1.2660    0.0220 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8599   -2.0944    0.0895 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6255   -1.3173    0.9449 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.1396   -1.1588    2.3790 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2617   -2.2955    0.8984 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3144    0.2409    0.3833 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3060    0.2021   -0.5316 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1000   -0.5545   -1.2435 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0643   -1.0820   -2.0873 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0803    0.9078   -1.3501 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.6447    1.1639   -2.6322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5900    1.8276   -0.3749 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6758    1.4086    0.9766 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5305   -3.3699    0.1390 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.0092   -1.5963    0.3742 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.3206   -2.6055    1.7596 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.2080   -2.8191    0.5261 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.7739   -1.1230    0.9995 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.5352   -0.5884   -1.1658 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.3193   -2.3072   -1.7328 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.9679   -2.1367   -1.7249 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.6818   -0.9545   -2.8004 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.8327    0.0743   -1.8446 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.1924    0.8776   -1.0556 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.7709   -0.5154    1.0361 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.4213   -1.3054    0.2014 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7987    0.5621    1.6631 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.7148    1.7236    0.6921 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.3045    1.1774   -1.3477 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3528    0.0758   -0.3183 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0278821 (PIP(PGD1/18:0))


  Mrv1652309132112542D          

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M  END
> <DATABASE_ID>
HMDB0278821

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCCCCCCCCCCC(=O)O[C@@H]1COC(=O)CCCCCC[C@H]2[C@@H](O)CC(=O)[C@H](\C=C\[C@@H](O)CCCCC)[C@@H](O)[C@@H](OP(O)(O)=O)[C@@H](OP(O)(=O)OC1)[C@H](O)[C@@H](O)[C@@H]2O

> <INCHI_IDENTIFIER>
InChI=1S/C47H86O19P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-24-28-41(52)64-35-32-62-40(51)27-23-20-19-22-26-36-38(49)31-39(50)37(30-29-34(48)25-21-6-4-2)43(54)46(65-67(57,58)59)47(45(56)44(55)42(36)53)66-68(60,61)63-33-35/h29-30,34-38,42-49,53-56H,3-28,31-33H2,1-2H3,(H,60,61)(H2,57,58,59)/b30-29+/t34-,35+,36-,37-,38-,42+,43+,44-,45+,46+,47-/m0/s1

> <INCHI_KEY>
ASIAYDFOQDKNJY-WDLBTPFPSA-N

> <FORMULA>
C47H86O19P2

> <MOLECULAR_WEIGHT>
1017.134

> <EXACT_MASS>
1016.523854545

> <JCHEM_ACCEPTOR_COUNT>
14

> <JCHEM_ATOM_COUNT>
154

> <JCHEM_AVERAGE_POLARIZABILITY>
109.8031414965396

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
9

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(1S,6R,16S,17S,20R,21R,22R,23R,24S,25R)-3,17,21,23,24,25-hexahydroxy-20-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-6-(octadecanoyloxy)-3,9,19-trioxo-2,4,8-trioxa-3lambda5-phosphabicyclo[14.6.3]pentacosan-22-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
3.48

> <JCHEM_LOGP>
6.975885471666666

> <ALOGPS_LOGS>
-4.11

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
1.89334082075482

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.9449079396812174

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3256131034329384

> <JCHEM_POLAR_SURFACE_AREA>
313.57

> <JCHEM_REFRACTIVITY>
251.9328000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
26

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
7.88e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(1S,6R,16S,17S,20R,21R,22R,23R,24S,25R)-3,17,21,23,24,25-hexahydroxy-20-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-6-(octadecanoyloxy)-3,9,19-trioxo-2,4,8-trioxa-3lambda5-phosphabicyclo[14.6.3]pentacosan-22-yl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0278821 (PIP(PGD1/18:0))

HMDB0278821
     RDKit          3D
PIP(PGD1/18:0)
154155  0  0  0  0  0  0  0  0999 V2000
   18.3520   -2.4352    0.6682 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8986   -2.0079    0.2972 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8548   -1.5017   -1.0814 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.5736   -1.1508   -1.6630 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.6706   -0.1239   -1.1083 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.0548   -0.3761    0.2214 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1380    0.7760    0.6398 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.9992    0.9885   -0.3145 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1748    2.1480    0.2368 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9978    2.4454   -0.6598 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0492    1.2946   -0.8161 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4720    0.9005    0.5427 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5240   -0.2557    0.3553 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9029   -0.6971    1.6586 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1105    0.4203    2.3061 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9897    0.8951    1.4065 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0142   -0.1885    1.0820 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9627    0.3550    0.1941 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3085    0.4725   -1.0327 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6933    0.7231    0.5969 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7846    1.2271   -0.3570 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.3421    2.6185   -0.1308 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8943    2.8064    0.4738 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4713    4.0325    0.7112 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1023    4.2050    1.7849 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3891    5.1689   -0.2365 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5377    5.1511   -1.2565 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7916    5.5150   -0.5628 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0622    5.3848   -1.3163 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2087    4.2492   -2.2469 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2061    3.1846   -1.8104 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9026    2.5462   -0.5180 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.0379    1.9380    0.2285 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.8762    2.9707    0.7797 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9949    1.0578   -0.4211 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6300   -0.1520   -1.0977 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4545   -0.0097   -2.3300 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4322   -1.5179   -0.5917 C   0  0  2  0  0  0  0  0  0  0  0  0
   -8.7652   -2.1698   -0.2727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2851   -3.1376   -0.9845 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5901   -3.7980   -0.6985 C   0  0  1  0  0  0  0  0  0  0  0  0
  -10.4859   -5.1867   -0.7602 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1562   -3.3550    0.6346 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4697   -4.0961    0.8001 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.1831   -3.7885    2.0775 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.4978   -2.3312    2.1503 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.3808   -1.9966    0.9542 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4726   -1.6802    0.5434 C   0  0  1  0  0  0  0  0  0  0  0  0
   -7.0829   -2.5855    1.4548 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.1514   -2.3033    0.1811 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.2472   -3.0653   -0.9814 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8559   -4.7002   -0.6929 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.6555   -5.1246   -1.4937 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1624   -5.7002   -1.0665 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.4434   -4.8989    0.9527 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0216   -1.2660    0.0220 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.8599   -2.0944    0.0895 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6255   -1.3173    0.9449 P   0  0  0  0  0  5  0  0  0  0  0  0
   -2.1396   -1.1588    2.3790 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2617   -2.2955    0.8984 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3144    0.2409    0.3833 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3060    0.2021   -0.5316 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.1000   -0.5545   -1.2435 C   0  0  2  0  0  0  0  0  0  0  0  0
   -3.0643   -1.0820   -2.0873 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0803    0.9078   -1.3501 C   0  0  1  0  0  0  0  0  0  0  0  0
   -4.6447    1.1639   -2.6322 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5900    1.8276   -0.3749 C   0  0  2  0  0  0  0  0  0  0  0  0
   -4.6758    1.4086    0.9766 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5305   -3.3699    0.1390 H   0  0  0  0  0  0  0  0  0  0  0  0
   19.0092   -1.5963    0.3742 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.3206   -2.6055    1.7596 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.2080   -2.8191    0.5261 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.7739   -1.1230    0.9995 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.5352   -0.5884   -1.1658 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.3193   -2.3072   -1.7328 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.9679   -2.1367   -1.7249 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.6818   -0.9545   -2.8004 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.8327    0.0743   -1.8446 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.1924    0.8776   -1.0556 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.7709   -0.5154    1.0361 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.4213   -1.3054    0.2014 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7987    0.5621    1.6631 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.7148    1.7236    0.6921 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.3045    1.1774   -1.3477 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3528    0.0758   -0.3183 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8687    1.8925    1.2520 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7966    3.0632    0.2670 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3506    2.7611   -1.6568 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.4322    3.2714   -0.1687 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5283    0.3984   -1.2507 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.2557    1.6053   -1.5079 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9838    1.8159    0.9315 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.2728    0.6248    1.2481 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7797   -0.0040   -0.4105 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1188   -1.1013   -0.0347 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7324   -0.9518    2.3507 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.3137   -1.6003    1.5029 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.6583    0.0262    3.2262 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.7792    1.2838    2.4849 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4469    1.6838    1.9652 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3350    1.3483    0.4737 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5080   -1.0696    0.5968 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5089   -0.6016    1.9826 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3344    1.2278   -1.3505 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1438    3.1366    0.4754 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3237    3.2200   -1.0874 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4077    6.1240    0.3028 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4172    5.1197   -0.7793 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -6.5826    1.5387    1.1889 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4666    2.5812    1.4696 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.6825    2.1493    1.6001 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
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
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 17 18  1  0
 18 19  2  0
 18 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  1  0
 23 24  1  0
 24 25  2  0
 24 26  1  0
 26 27  1  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  1  0
 33 35  1  0
 35 36  1  0
 36 37  2  0
 36 38  1  0
 38 39  1  0
 39 40  2  0
 40 41  1  0
 41 42  1  0
 41 43  1  0
 43 44  1  0
 44 45  1  0
 45 46  1  0
 46 47  1  0
 38 48  1  0
 48 49  1  0
 48 50  1  0
 50 51  1  0
 51 52  1  0
 52 53  2  0
 52 54  1  0
 52 55  1  0
 50 56  1  0
 56 57  1  0
 57 58  1  0
 58 59  2  0
 58 60  1  0
 58 61  1  0
 61 62  1  0
 56 63  1  0
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 67 68  1  0
 62 21  1  0
 67 32  1  0
  1 69  1  0
  1 70  1  0
  1 71  1  0
  2 72  1  0
  2 73  1  0
  3 74  1  0
  3 75  1  0
  4 76  1  0
  4 77  1  0
  5 78  1  0
  5 79  1  0
  6 80  1  0
  6 81  1  0
  7 82  1  0
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  9 87  1  0
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 16100  1  0
 16101  1  0
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 65151  1  6
 66152  1  0
 67153  1  1
 68154  1  0
M  END
Download

PDB for HMDB0278821 (PIP(PGD1/18:0))

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       3.107  11.538   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       1.735  11.202   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.253  12.653   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.298  13.971   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.792  12.609   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.681  14.238   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.226  11.131   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       5.204  10.311   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0       5.160   8.772   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0       6.748   9.913   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       7.215   8.967   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       6.472   7.964   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0       6.845   6.300   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       8.157   5.492   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0       8.113   3.953   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0       6.758   3.221   0.000  0.00  0.00           O+0
HETATM   17  C   UNK     0       5.447   4.029   0.000  0.00  0.00           C+0
HETATM   18  O   UNK     0       6.795   4.964   0.000  0.00  0.00           O+0
HETATM   19  C   UNK     0       4.092   3.297   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0       2.780   4.104   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0       2.824   5.644   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       1.513   6.451   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0       1.139   8.115   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      -0.172   8.923   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       0.289  10.338   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0       0.475   8.730   0.000  0.00  0.00           C+0
HETATM   27  O   UNK     0      -0.940   7.699   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       1.786   7.922   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       2.911   8.723   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0       2.113  10.221   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0       4.223   7.915   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0       3.349   6.345   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0       3.658   4.596   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0       2.905   2.916   0.000  0.00  0.00           C+0
HETATM   35  O   UNK     0       1.147   3.308   0.000  0.00  0.00           O+0
HETATM   36  C   UNK     0       3.331   1.219   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       2.482  -0.139   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0       0.924   0.097   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0      -0.261  -0.870   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      -1.701  -0.324   0.000  0.00  0.00           C+0
HETATM   41  O   UNK     0       9.857   5.430   0.000  0.00  0.00           O+0
HETATM   42  C   UNK     0      11.414   4.890   0.000  0.00  0.00           C+0
HETATM   43  O   UNK     0      11.768   3.357   0.000  0.00  0.00           O+0
HETATM   44  C   UNK     0      12.565   6.084   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      13.884   5.129   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      15.097   6.146   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      16.349   5.174   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      17.635   6.097   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      18.899   5.138   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      20.242   5.971   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      21.520   5.036   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      22.862   5.885   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      24.189   5.018   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      25.573   5.798   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      26.911   4.939   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      28.325   5.666   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      29.717   4.890   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      31.134   5.628   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      32.550   4.890   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      33.925   5.662   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0       5.851  10.118   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0       7.063  11.635   0.000  0.00  0.00           O+0
HETATM   63  P   UNK     0       8.055  13.081   0.000  0.00  0.00           P+0
HETATM   64  O   UNK     0       9.647  13.427   0.000  0.00  0.00           O+0
HETATM   65  O   UNK     0       6.991  14.251   0.000  0.00  0.00           O+0
HETATM   66  O   UNK     0       8.697  14.616   0.000  0.00  0.00           O+0
HETATM   67  C   UNK     0       5.807   8.578   0.000  0.00  0.00           C+0
HETATM   68  O   UNK     0       7.523   7.721   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3   25                                                  
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   41                                                  
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    2   26                                                  
CONECT   26   25   27   28                                                  
CONECT   27   26                                                            
CONECT   28   26   29                                                       
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32   67                                                  
CONECT   32   31   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35   36                                                  
CONECT   35   34                                                            
CONECT   36   34   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39                                                            
CONECT   41   14   42                                                       
CONECT   42   41   43   44                                                  
CONECT   43   42                                                            
CONECT   44   42   45                                                       
CONECT   45   44   46                                                       
CONECT   46   45   47                                                       
CONECT   47   46   48                                                       
CONECT   48   47   49                                                       
CONECT   49   48   50                                                       
CONECT   50   49   51                                                       
CONECT   51   50   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59                                                            
CONECT   61    7   62   67                                                  
CONECT   62   61   63                                                       
CONECT   63   62   64   65   66                                             
CONECT   64   63                                                            
CONECT   65   63                                                            
CONECT   66   63                                                            
CONECT   67   61   31   68                                                  
CONECT   68   67                                                            
MASTER        0    0    0    0    0    0    0    0   68    0  138    0
END
Download

3D PDB for HMDB0278821 (PIP(PGD1/18:0))

COMPND    HMDB0278821
HETATM    1  C1  UNL     1      18.352  -2.435   0.668  1.00  0.00           C  
HETATM    2  C2  UNL     1      16.899  -2.008   0.297  1.00  0.00           C  
HETATM    3  C3  UNL     1      16.855  -1.502  -1.081  1.00  0.00           C  
HETATM    4  C4  UNL     1      15.574  -1.151  -1.663  1.00  0.00           C  
HETATM    5  C5  UNL     1      14.671  -0.124  -1.108  1.00  0.00           C  
HETATM    6  C6  UNL     1      14.055  -0.376   0.221  1.00  0.00           C  
HETATM    7  C7  UNL     1      13.138   0.776   0.640  1.00  0.00           C  
HETATM    8  C8  UNL     1      11.999   0.989  -0.315  1.00  0.00           C  
HETATM    9  C9  UNL     1      11.175   2.148   0.237  1.00  0.00           C  
HETATM   10  C10 UNL     1       9.998   2.445  -0.660  1.00  0.00           C  
HETATM   11  C11 UNL     1       9.049   1.295  -0.816  1.00  0.00           C  
HETATM   12  C12 UNL     1       8.472   0.901   0.543  1.00  0.00           C  
HETATM   13  C13 UNL     1       7.524  -0.256   0.355  1.00  0.00           C  
HETATM   14  C14 UNL     1       6.903  -0.697   1.659  1.00  0.00           C  
HETATM   15  C15 UNL     1       6.111   0.420   2.306  1.00  0.00           C  
HETATM   16  C16 UNL     1       4.990   0.895   1.406  1.00  0.00           C  
HETATM   17  C17 UNL     1       4.014  -0.188   1.082  1.00  0.00           C  
HETATM   18  C18 UNL     1       2.963   0.355   0.194  1.00  0.00           C  
HETATM   19  O1  UNL     1       3.309   0.472  -1.033  1.00  0.00           O  
HETATM   20  O2  UNL     1       1.693   0.723   0.597  1.00  0.00           O  
HETATM   21  C19 UNL     1       0.785   1.227  -0.357  1.00  0.00           C  
HETATM   22  C20 UNL     1       0.342   2.618  -0.131  1.00  0.00           C  
HETATM   23  O3  UNL     1      -0.894   2.806   0.474  1.00  0.00           O  
HETATM   24  C21 UNL     1      -1.471   4.033   0.711  1.00  0.00           C  
HETATM   25  O4  UNL     1      -2.102   4.205   1.785  1.00  0.00           O  
HETATM   26  C22 UNL     1      -1.389   5.169  -0.236  1.00  0.00           C  
HETATM   27  C23 UNL     1      -2.538   5.151  -1.257  1.00  0.00           C  
HETATM   28  C24 UNL     1      -3.792   5.515  -0.563  1.00  0.00           C  
HETATM   29  C25 UNL     1      -5.062   5.385  -1.316  1.00  0.00           C  
HETATM   30  C26 UNL     1      -5.209   4.249  -2.247  1.00  0.00           C  
HETATM   31  C27 UNL     1      -6.206   3.185  -1.810  1.00  0.00           C  
HETATM   32  C28 UNL     1      -5.903   2.546  -0.518  1.00  0.00           C  
HETATM   33  C29 UNL     1      -7.038   1.938   0.229  1.00  0.00           C  
HETATM   34  O5  UNL     1      -7.876   2.971   0.780  1.00  0.00           O  
HETATM   35  C30 UNL     1      -7.995   1.058  -0.421  1.00  0.00           C  
HETATM   36  C31 UNL     1      -7.630  -0.152  -1.098  1.00  0.00           C  
HETATM   37  O6  UNL     1      -7.454  -0.010  -2.330  1.00  0.00           O  
HETATM   38  C32 UNL     1      -7.432  -1.518  -0.592  1.00  0.00           C  
HETATM   39  C33 UNL     1      -8.765  -2.170  -0.273  1.00  0.00           C  
HETATM   40  C34 UNL     1      -9.285  -3.138  -0.984  1.00  0.00           C  
HETATM   41  C35 UNL     1     -10.590  -3.798  -0.699  1.00  0.00           C  
HETATM   42  O7  UNL     1     -10.486  -5.187  -0.760  1.00  0.00           O  
HETATM   43  C36 UNL     1     -11.156  -3.355   0.635  1.00  0.00           C  
HETATM   44  C37 UNL     1     -12.470  -4.096   0.800  1.00  0.00           C  
HETATM   45  C38 UNL     1     -13.183  -3.789   2.078  1.00  0.00           C  
HETATM   46  C39 UNL     1     -13.498  -2.331   2.150  1.00  0.00           C  
HETATM   47  C40 UNL     1     -14.381  -1.997   0.954  1.00  0.00           C  
HETATM   48  C41 UNL     1      -6.473  -1.680   0.543  1.00  0.00           C  
HETATM   49  O8  UNL     1      -7.083  -2.586   1.455  1.00  0.00           O  
HETATM   50  C42 UNL     1      -5.151  -2.303   0.181  1.00  0.00           C  
HETATM   51  O9  UNL     1      -5.247  -3.065  -0.981  1.00  0.00           O  
HETATM   52  P1  UNL     1      -4.856  -4.700  -0.693  1.00  0.00           P  
HETATM   53  O10 UNL     1      -3.655  -5.125  -1.494  1.00  0.00           O  
HETATM   54  O11 UNL     1      -6.162  -5.700  -1.067  1.00  0.00           O  
HETATM   55  O12 UNL     1      -4.443  -4.899   0.953  1.00  0.00           O  
HETATM   56  C43 UNL     1      -4.022  -1.266   0.022  1.00  0.00           C  
HETATM   57  O13 UNL     1      -2.860  -2.094   0.090  1.00  0.00           O  
HETATM   58  P2  UNL     1      -1.625  -1.317   0.945  1.00  0.00           P  
HETATM   59  O14 UNL     1      -2.140  -1.159   2.379  1.00  0.00           O  
HETATM   60  O15 UNL     1      -0.262  -2.296   0.898  1.00  0.00           O  
HETATM   61  O16 UNL     1      -1.314   0.241   0.383  1.00  0.00           O  
HETATM   62  C44 UNL     1      -0.306   0.202  -0.532  1.00  0.00           C  
HETATM   63  C45 UNL     1      -4.100  -0.555  -1.244  1.00  0.00           C  
HETATM   64  O17 UNL     1      -3.064  -1.082  -2.087  1.00  0.00           O  
HETATM   65  C46 UNL     1      -4.080   0.908  -1.350  1.00  0.00           C  
HETATM   66  O18 UNL     1      -4.645   1.164  -2.632  1.00  0.00           O  
HETATM   67  C47 UNL     1      -4.590   1.828  -0.375  1.00  0.00           C  
HETATM   68  O19 UNL     1      -4.676   1.409   0.977  1.00  0.00           O  
HETATM   69  H1  UNL     1      18.531  -3.370   0.139  1.00  0.00           H  
HETATM   70  H2  UNL     1      19.009  -1.596   0.374  1.00  0.00           H  
HETATM   71  H3  UNL     1      18.321  -2.605   1.760  1.00  0.00           H  
HETATM   72  H4  UNL     1      16.208  -2.819   0.526  1.00  0.00           H  
HETATM   73  H5  UNL     1      16.774  -1.123   0.999  1.00  0.00           H  
HETATM   74  H6  UNL     1      17.535  -0.588  -1.166  1.00  0.00           H  
HETATM   75  H7  UNL     1      17.319  -2.307  -1.733  1.00  0.00           H  
HETATM   76  H8  UNL     1      14.968  -2.137  -1.725  1.00  0.00           H  
HETATM   77  H9  UNL     1      15.682  -0.955  -2.800  1.00  0.00           H  
HETATM   78  H10 UNL     1      13.833   0.074  -1.845  1.00  0.00           H  
HETATM   79  H11 UNL     1      15.192   0.878  -1.056  1.00  0.00           H  
HETATM   80  H12 UNL     1      14.771  -0.515   1.036  1.00  0.00           H  
HETATM   81  H13 UNL     1      13.421  -1.305   0.201  1.00  0.00           H  
HETATM   82  H14 UNL     1      12.799   0.562   1.663  1.00  0.00           H  
HETATM   83  H15 UNL     1      13.715   1.724   0.692  1.00  0.00           H  
HETATM   84  H16 UNL     1      12.305   1.177  -1.348  1.00  0.00           H  
HETATM   85  H17 UNL     1      11.353   0.076  -0.318  1.00  0.00           H  
HETATM   86  H18 UNL     1      10.869   1.892   1.252  1.00  0.00           H  
HETATM   87  H19 UNL     1      11.797   3.063   0.267  1.00  0.00           H  
HETATM   88  H20 UNL     1      10.351   2.761  -1.657  1.00  0.00           H  
HETATM   89  H21 UNL     1       9.432   3.271  -0.169  1.00  0.00           H  
HETATM   90  H22 UNL     1       9.528   0.398  -1.251  1.00  0.00           H  
HETATM   91  H23 UNL     1       8.256   1.605  -1.508  1.00  0.00           H  
HETATM   92  H24 UNL     1       7.984   1.816   0.931  1.00  0.00           H  
HETATM   93  H25 UNL     1       9.273   0.625   1.248  1.00  0.00           H  
HETATM   94  H26 UNL     1       6.780  -0.004  -0.410  1.00  0.00           H  
HETATM   95  H27 UNL     1       8.119  -1.101  -0.035  1.00  0.00           H  
HETATM   96  H28 UNL     1       7.732  -0.952   2.351  1.00  0.00           H  
HETATM   97  H29 UNL     1       6.314  -1.600   1.503  1.00  0.00           H  
HETATM   98  H30 UNL     1       5.658   0.026   3.226  1.00  0.00           H  
HETATM   99  H31 UNL     1       6.779   1.284   2.485  1.00  0.00           H  
HETATM  100  H32 UNL     1       4.447   1.684   1.965  1.00  0.00           H  
HETATM  101  H33 UNL     1       5.335   1.348   0.474  1.00  0.00           H  
HETATM  102  H34 UNL     1       4.508  -1.070   0.597  1.00  0.00           H  
HETATM  103  H35 UNL     1       3.509  -0.602   1.983  1.00  0.00           H  
HETATM  104  H36 UNL     1       1.334   1.228  -1.350  1.00  0.00           H  
HETATM  105  H37 UNL     1       1.144   3.137   0.475  1.00  0.00           H  
HETATM  106  H38 UNL     1       0.324   3.220  -1.087  1.00  0.00           H  
HETATM  107  H39 UNL     1      -1.408   6.124   0.303  1.00  0.00           H  
HETATM  108  H40 UNL     1      -0.417   5.120  -0.779  1.00  0.00           H  
HETATM  109  H41 UNL     1      -2.225   5.864  -2.046  1.00  0.00           H  
HETATM  110  H42 UNL     1      -2.549   4.104  -1.608  1.00  0.00           H  
HETATM  111  H43 UNL     1      -3.841   4.934   0.406  1.00  0.00           H  
HETATM  112  H44 UNL     1      -3.641   6.578  -0.183  1.00  0.00           H  
HETATM  113  H45 UNL     1      -5.925   5.378  -0.584  1.00  0.00           H  
HETATM  114  H46 UNL     1      -5.213   6.385  -1.832  1.00  0.00           H  
HETATM  115  H47 UNL     1      -5.698   4.671  -3.186  1.00  0.00           H  
HETATM  116  H48 UNL     1      -4.263   3.861  -2.598  1.00  0.00           H  
HETATM  117  H49 UNL     1      -6.517   2.545  -2.636  1.00  0.00           H  
HETATM  118  H50 UNL     1      -7.142   3.806  -1.615  1.00  0.00           H  
HETATM  119  H51 UNL     1      -5.742   3.491   0.135  1.00  0.00           H  
HETATM  120  H52 UNL     1      -6.583   1.539   1.189  1.00  0.00           H  
HETATM  121  H53 UNL     1      -8.467   2.581   1.470  1.00  0.00           H  
HETATM  122  H54 UNL     1      -8.667   1.716  -1.064  1.00  0.00           H  
HETATM  123  H55 UNL     1      -8.727   0.754   0.398  1.00  0.00           H  
HETATM  124  H56 UNL     1      -7.000  -2.189  -1.397  1.00  0.00           H  
HETATM  125  H57 UNL     1      -9.298  -1.803   0.592  1.00  0.00           H  
HETATM  126  H58 UNL     1      -8.684  -3.463  -1.852  1.00  0.00           H  
HETATM  127  H59 UNL     1     -11.307  -3.514  -1.519  1.00  0.00           H  
HETATM  128  H60 UNL     1     -10.202  -5.487   0.141  1.00  0.00           H  
HETATM  129  H61 UNL     1     -10.465  -3.724   1.421  1.00  0.00           H  
HETATM  130  H62 UNL     1     -11.271  -2.274   0.695  1.00  0.00           H  
HETATM  131  H63 UNL     1     -13.101  -3.864  -0.082  1.00  0.00           H  
HETATM  132  H64 UNL     1     -12.297  -5.192   0.769  1.00  0.00           H  
HETATM  133  H65 UNL     1     -14.143  -4.345   2.050  1.00  0.00           H  
HETATM  134  H66 UNL     1     -12.588  -4.159   2.937  1.00  0.00           H  
HETATM  135  H67 UNL     1     -12.556  -1.758   2.167  1.00  0.00           H  
HETATM  136  H68 UNL     1     -14.119  -2.080   3.059  1.00  0.00           H  
HETATM  137  H69 UNL     1     -13.809  -1.942   0.021  1.00  0.00           H  
HETATM  138  H70 UNL     1     -14.869  -1.036   1.129  1.00  0.00           H  
HETATM  139  H71 UNL     1     -15.102  -2.853   0.872  1.00  0.00           H  
HETATM  140  H72 UNL     1      -6.267  -0.797   1.139  1.00  0.00           H  
HETATM  141  H73 UNL     1      -6.727  -2.432   2.381  1.00  0.00           H  
HETATM  142  H74 UNL     1      -4.828  -3.012   0.994  1.00  0.00           H  
HETATM  143  H75 UNL     1      -6.380  -6.247  -0.291  1.00  0.00           H  
HETATM  144  H76 UNL     1      -5.253  -4.987   1.515  1.00  0.00           H  
HETATM  145  H77 UNL     1      -3.943  -0.735   0.968  1.00  0.00           H  
HETATM  146  H78 UNL     1       0.123  -2.362   1.816  1.00  0.00           H  
HETATM  147  H79 UNL     1       0.134  -0.817  -0.549  1.00  0.00           H  
HETATM  148  H80 UNL     1      -0.766   0.308  -1.559  1.00  0.00           H  
HETATM  149  H81 UNL     1      -4.974  -1.007  -1.817  1.00  0.00           H  
HETATM  150  H82 UNL     1      -3.265  -0.906  -3.019  1.00  0.00           H  
HETATM  151  H83 UNL     1      -2.987   1.171  -1.577  1.00  0.00           H  
HETATM  152  H84 UNL     1      -4.057   0.939  -3.360  1.00  0.00           H  
HETATM  153  H85 UNL     1      -3.801   2.644  -0.229  1.00  0.00           H  
HETATM  154  H86 UNL     1      -4.682   2.149   1.600  1.00  0.00           H  
CONECT    1    2   69   70   71
CONECT    2    3   72   73
CONECT    3    4   74   75
CONECT    4    5   76   77
CONECT    5    6   78   79
CONECT    6    7   80   81
CONECT    7    8   82   83
CONECT    8    9   84   85
CONECT    9   10   86   87
CONECT   10   11   88   89
CONECT   11   12   90   91
CONECT   12   13   92   93
CONECT   13   14   94   95
CONECT   14   15   96   97
CONECT   15   16   98   99
CONECT   16   17  100  101
CONECT   17   18  102  103
CONECT   18   19   19   20
CONECT   20   21
CONECT   21   22   62  104
CONECT   22   23  105  106
CONECT   23   24
CONECT   24   25   25   26
CONECT   26   27  107  108
CONECT   27   28  109  110
CONECT   28   29  111  112
CONECT   29   30  113  114
CONECT   30   31  115  116
CONECT   31   32  117  118
CONECT   32   33   67  119
CONECT   33   34   35  120
CONECT   34  121
CONECT   35   36  122  123
CONECT   36   37   37   38
CONECT   38   39   48  124
CONECT   39   40   40  125
CONECT   40   41  126
CONECT   41   42   43  127
CONECT   42  128
CONECT   43   44  129  130
CONECT   44   45  131  132
CONECT   45   46  133  134
CONECT   46   47  135  136
CONECT   47  137  138  139
CONECT   48   49   50  140
CONECT   49  141
CONECT   50   51   56  142
CONECT   51   52
CONECT   52   53   53   54   55
CONECT   54  143
CONECT   55  144
CONECT   56   57   63  145
CONECT   57   58
CONECT   58   59   59   60   61
CONECT   60  146
CONECT   61   62
CONECT   62  147  148
CONECT   63   64   65  149
CONECT   64  150
CONECT   65   66   67  151
CONECT   66  152
CONECT   67   68  153
CONECT   68  154
END
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SMILES for HMDB0278821 (PIP(PGD1/18:0))

CCCCCCCCCCCCCCCCCC(=O)O[C@@H]1COC(=O)CCCCCC[C@H]2[C@@H](O)CC(=O)[C@H](\C=C\[C@@H](O)CCCCC)[C@@H](O)[C@@H](OP(O)(O)=O)[C@@H](OP(O)(=O)OC1)[C@H](O)[C@@H](O)[C@@H]2O
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INCHI for HMDB0278821 (PIP(PGD1/18:0))

InChI=1S/C47H86O19P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-24-28-41(52)64-35-32-62-40(51)27-23-20-19-22-26-36-38(49)31-39(50)37(30-29-34(48)25-21-6-4-2)43(54)46(65-67(57,58)59)47(45(56)44(55)42(36)53)66-68(60,61)63-33-35/h29-30,34-38,42-49,53-56H,3-28,31-33H2,1-2H3,(H,60,61)(H2,57,58,59)/b30-29+/t34-,35+,36-,37-,38-,42+,43+,44-,45+,46+,47-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
{[(1S,6R,16S,17S,20R,21R,22R,23R,24S,25R)-3,17,21,23,24,25-hexahydroxy-20-[(3S)-3-hydroxyoct-1-en-1-yl]-6-(octadecanoyloxy)-3,9,19-trioxo-2,4,8-trioxa-3-phosphabicyclo[14.6.3]pentacosan-22-yl]oxy}phosphonateHMDB
Chemical FormulaC47H86O19P2
Average Molecular Weight1017.134
Monoisotopic Molecular Weight1016.523854545
IUPAC Name{[(1S,6R,16S,17S,20R,21R,22R,23R,24S,25R)-3,17,21,23,24,25-hexahydroxy-20-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-6-(octadecanoyloxy)-3,9,19-trioxo-2,4,8-trioxa-3lambda5-phosphabicyclo[14.6.3]pentacosan-22-yl]oxy}phosphonic acid
Traditional Name[(1S,6R,16S,17S,20R,21R,22R,23R,24S,25R)-3,17,21,23,24,25-hexahydroxy-20-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-6-(octadecanoyloxy)-3,9,19-trioxo-2,4,8-trioxa-3lambda5-phosphabicyclo[14.6.3]pentacosan-22-yl]oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCCCCCCC(=O)O[C@@H]1COC(=O)CCCCCC[C@H]2[C@@H](O)CC(=O)[C@H](\C=C\[C@@H](O)CCCCC)[C@@H](O)[C@@H](OP(O)(O)=O)[C@@H](OP(O)(=O)OC1)[C@H](O)[C@@H](O)[C@@H]2O
InChI Identifier
InChI=1S/C47H86O19P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-24-28-41(52)64-35-32-62-40(51)27-23-20-19-22-26-36-38(49)31-39(50)37(30-29-34(48)25-21-6-4-2)43(54)46(65-67(57,58)59)47(45(56)44(55)42(36)53)66-68(60,61)63-33-35/h29-30,34-38,42-49,53-56H,3-28,31-33H2,1-2H3,(H,60,61)(H2,57,58,59)/b30-29+/t34-,35+,36-,37-,38-,42+,43+,44-,45+,46+,47-/m0/s1
InChI KeyASIAYDFOQDKNJY-WDLBTPFPSA-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
  • Monoalkyl phosphate
  • Fatty acid ester
  • Fatty acyl
  • Alkyl phosphate
  • Phosphoric acid ester
  • 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
logP3.48ALOGPS
logP6.98ChemAxon
logS-4.1ALOGPS
pKa (Strongest Acidic)0.94ChemAxon
pKa (Strongest Basic)-3.3ChemAxon
Physiological Charge-3ChemAxon
Hydrogen Acceptor Count14ChemAxon
Hydrogen Donor Count9ChemAxon
Polar Surface Area313.57 ŲChemAxon
Rotatable Bond Count26ChemAxon
Refractivity251.93 m³·mol⁻¹ChemAxon
Polarizability109.8 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]+309.43532859911
AllCCS[M+H-H2O]+309.86732859911
AllCCS[M+Na]+308.87232859911
AllCCS[M+NH4]+309.00232859911
AllCCS[M-H]-319.35432859911
AllCCS[M+Na-2H]-325.10132859911
AllCCS[M+HCOO]-331.40432859911
DeepCCS[M+H]+311.96530932474
DeepCCS[M-H]-310.31230932474
DeepCCS[M-2H]-344.34830932474
DeepCCS[M+Na]+318.12230932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PIP(PGD1/18:0) 10V, Positive-QTOFsplash10-014j-9000000008-9b5db10fde77309840722021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PIP(PGD1/18:0) 20V, Positive-QTOFsplash10-00kb-4000000019-5cd7e97b7dd94c40f0a82021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PIP(PGD1/18:0) 40V, Positive-QTOFsplash10-0ul9-4200000900-1d4d1de2f90a262a62dc2021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PIP(PGD1/18:0) 10V, Negative-QTOFsplash10-014i-9000000001-11bfe2922f43393e3af62021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PIP(PGD1/18:0) 20V, Negative-QTOFsplash10-015a-9020000601-fff16fd69e2cedec4ab02021-10-19Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PIP(PGD1/18:0) 40V, Negative-QTOFsplash10-00lr-3010004900-147a16d08f1c3c46f7a52021-10-19Wishart 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 Compound156982173
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