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Showing metabocard for PG(5-iso PGF2VI/a-21:0) (HMDB0270886)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-12 18:41:10 UTC
Update Date2022-11-30 19:58:15 UTC
HMDB IDHMDB0270886
Secondary Accession NumbersNone
Metabolite Identification
Common NamePG(5-iso PGF2VI/a-21:0)
DescriptionPG(5-iso PGF2VI/a-21:0) is an oxidized phosphatidylglycerol (PG). Oxidized phosphatidylglycerols are glycerophospholipids in which a phosphoglycerol moiety occupies a glycerol substitution site and at least one of the fatty acyl chains has undergone oxidation. As all oxidized lipids, oxidized phosphatidylglycerols belong to a group of biomolecules that have a role as signaling molecules. The biosynthesis of oxidized lipids is mediated by several enzymatic families, including cyclooxygenases (COX), lipoxygenases (LOX) and cytochrome P450s (CYP). Non-enzymatically oxidized lipids are produced by uncontrolled oxidation through free radicals and are considered harmful to human health (PMID: 33329396 ). As is the case with diacylglycerols, phosphatidylglycerols can have many different combinations of fatty acids of varying lengths, saturation and degrees of oxidation attached at the C-1 and C-2 positions. PG(5-iso PGF2VI/a-21:0), in particular, consists of one chain of one 5-iso Prostaglandin F2alpha-VI at the C-1 position and one chain of 18-methyleicosanoyl at the C-2 position. Phospholipids are ubiquitous in nature and are key components of the lipid bilayer of cells, as well as being involved in metabolism and signaling. Similarly to what occurs with phospholipids, the fatty acid distribution at the C-1 and C-2 positions of glycerol within oxidized phospholipids is continually in flux, owing to phospholipid degradation and the continuous phospholipid remodeling that occurs while these molecules are in membranes. Oxidized PGs can be synthesized via three different routes. In one route, the oxidized PG is synthetized de novo following the same mechanisms as for PGs but incorporating oxidized acyl chains (PMID: 33329396 ). An alternative is the transacylation of one of the non-oxidized acyl chains with an oxidized acylCoA (PMID: 33329396 ). The third pathway results from the oxidation of the acyl chain while still attached to the PG backbone, mainly through the action of LOX (PMID: 33329396 ).
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0270886 (PG(5-iso PGF2VI/a-21:0))


  Mrv1652309122120412D          

 59 59  0  0  1  0            999 V2000
    5.1218   -7.9713    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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 58 59  1  0  0  0  0
M  END
Download

3D MOL for HMDB0270886 (PG(5-iso PGF2VI/a-21:0))

HMDB0270886
     RDKit          3D
PG(5-iso PGF2VI/a-21:0)
142142  0  0  0  0  0  0  0  0999 V2000
   15.0237    2.0341    0.0305 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8865    3.4587    0.5254 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5334    4.0270    0.2430 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4318    3.2173    0.9214 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0724    3.8064    0.6156 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0072    2.9817    1.3028 C   0  0  1  0  0  0  0  0  0  0  0  0
   10.2089    2.9869    2.6706 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6403    3.4623    0.9403 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.2037    3.5050   -0.2980 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8595    3.9707   -0.7331 C   0  0  2  0  0  0  0  0  0  0  0  0
    6.2247    3.0231   -1.7544 C   0  0  2  0  0  0  0  0  0  0  0  0
    5.8107    1.7385   -1.1360 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.2062    0.7548   -2.0226 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9761    0.3242   -1.8760 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1036    0.8061   -0.8061 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.6502   -0.2515    0.1463 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4857   -0.1521    0.5977 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4273   -1.3063    0.5471 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1056   -2.3444    1.4146 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0488   -3.2405    0.8355 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6362   -3.7427   -0.5012 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8120   -4.4166   -0.2883 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4362   -4.9499   -1.7560 P   0  0  0  0  0  5  0  0  0  0  0  0
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    4.8321   -6.5763   -1.6225 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.2522   -2.1653    1.4402 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2760   -1.9437   -0.0119 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -9.6600   -2.4906   -0.2184 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0312   -2.3529   -0.7261 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.7807    4.4212   -2.8491 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.8893    5.6172   -2.0681 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.8023    1.3115    0.8341 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.2867    1.8865   -0.7655 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.0661    1.8909   -0.3212 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.0363    3.4827    1.6330 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.6452    4.1068    0.0456 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.3287    4.1103   -0.8430 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.4869    5.0402    0.6661 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.6234    3.1734    2.0154 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.4949    2.1863    0.5135 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8645    3.7678   -0.4731 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.0742    4.8555    0.9417 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.1199    1.9419    0.9440 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8810    3.6448    2.9587 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9771    3.7899    1.7286 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.8841    3.1732   -1.0736 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1977    4.2253    0.0878 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3628    3.6118   -2.1639 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.3101    1.9500   -0.1910 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.8043    1.2584   -0.7874 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8161    0.3494   -2.8649 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5664   -0.4362   -2.5864 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.1269    1.1348   -1.3190 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4091    1.6967   -0.2671 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0494   -2.9318    1.6100 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8164   -1.9799    2.4330 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8813   -4.1327    1.5064 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7794   -2.8556   -1.1456 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.8414   -4.3591   -0.9872 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8888   -5.5807   -3.1763 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6553   -6.8557    0.0612 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.4140   -6.4086    0.3729 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.1147   -8.5185   -0.6538 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0270886 (PG(5-iso PGF2VI/a-21:0))


  Mrv1652309122120412D          

 59 59  0  0  1  0            999 V2000
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M  END
> <DATABASE_ID>
HMDB0270886

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCC[C@@H](O)\C=C\[C@H]1[C@H](O)C[C@H](O)[C@H]1C\C=C/CC(=O)OC[C@H](COP(O)(=O)OC[C@@H](O)CO)OC(=O)CCCCCCCCCCCCCCCCC(C)CC

> <INCHI_IDENTIFIER>
InChI=1S/C45H83O13P/c1-4-6-19-25-37(47)29-30-41-40(42(49)31-43(41)50)26-22-23-27-44(51)55-34-39(35-57-59(53,54)56-33-38(48)32-46)58-45(52)28-21-18-16-14-12-10-8-7-9-11-13-15-17-20-24-36(3)5-2/h22-23,29-30,36-43,46-50H,4-21,24-28,31-35H2,1-3H3,(H,53,54)/b23-22-,30-29+/t36?,37-,38+,39-,40+,41-,42+,43-/m1/s1

> <INCHI_KEY>
OAOOSHIMLCCREY-KIVQXAQVSA-N

> <FORMULA>
C45H83O13P

> <MOLECULAR_WEIGHT>
863.12

> <EXACT_MASS>
862.557129731

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
142

> <JCHEM_AVERAGE_POLARIZABILITY>
101.34241565463607

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
[(2R)-3-{[(3Z)-5-[(1S,2R,3R,5S)-3,5-dihydroxy-2-[(1E,3R)-3-hydroxyoct-1-en-1-yl]cyclopentyl]pent-3-enoyl]oxy}-2-[(18-methylicosanoyl)oxy]propoxy][(2S)-2,3-dihydroxypropoxy]phosphinic acid

> <ALOGPS_LOGP>
6.29

> <JCHEM_LOGP>
8.467679585333332

> <ALOGPS_LOGS>
-6.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-1

> <JCHEM_PKA>
13.586611654574046

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.8909057940334373

> <JCHEM_PKA_STRONGEST_BASIC>
-1.6264437319451166

> <JCHEM_POLAR_SURFACE_AREA>
209.50999999999996

> <JCHEM_REFRACTIVITY>
232.44660000000007

> <JCHEM_ROTATABLE_BOND_COUNT>
40

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.65e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-3-{[(3Z)-5-[(1S,2R,3R,5S)-3,5-dihydroxy-2-[(1E,3R)-3-hydroxyoct-1-en-1-yl]cyclopentyl]pent-3-enoyl]oxy}-2-[(18-methylicosanoyl)oxy]propoxy((2S)-2,3-dihydroxypropoxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0270886 (PG(5-iso PGF2VI/a-21:0))

HMDB0270886
     RDKit          3D
PG(5-iso PGF2VI/a-21:0)
142142  0  0  0  0  0  0  0  0999 V2000
   15.0237    2.0341    0.0305 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8865    3.4587    0.5254 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5334    4.0270    0.2430 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0270886 (PG(5-iso PGF2VI/a-21:0))

HEADER    PROTEIN                                 12-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   12-SEP-21         0                                  
HETATM    1  O   UNK     0       9.561 -14.880   0.000  0.00  0.00           O+0
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HETATM    4  O   UNK     0       6.893 -13.340   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       8.227 -11.030   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.893 -10.260   0.000  0.00  0.00           O+0
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HETATM   20  C   UNK     0       0.225  -6.410   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -1.109  -7.180   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      -1.270  -8.711   0.000  0.00  0.00           C+0
HETATM   23  O   UNK     0      -0.125  -9.742   0.000  0.00  0.00           O+0
HETATM   24  C   UNK     0      -2.776  -9.032   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      -3.546  -7.698   0.000  0.00  0.00           C+0
HETATM   26  O   UNK     0      -5.078  -7.537   0.000  0.00  0.00           O+0
HETATM   27  C   UNK     0      -2.516  -6.553   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      -2.836  -5.047   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      -1.691  -4.017   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      -2.012  -2.510   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      -3.476  -2.034   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -0.867  -1.480   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      -1.187   0.027   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      -0.043   1.057   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      -0.363   2.563   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0       0.781   3.594   0.000  0.00  0.00           C+0
HETATM   37  O   UNK     0       9.561  -4.100   0.000  0.00  0.00           O+0
HETATM   38  C   UNK     0      10.894  -4.870   0.000  0.00  0.00           C+0
HETATM   39  O   UNK     0      10.894  -6.410   0.000  0.00  0.00           O+0
HETATM   40  C   UNK     0      12.228  -4.100   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      13.562  -4.870   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      14.895  -4.100   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      16.229  -4.870   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0      17.563  -4.100   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0      18.896  -4.870   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0      20.230  -4.100   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0      21.564  -4.870   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0      22.897  -4.100   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0      24.231  -4.870   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0      25.565  -4.100   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0      26.899  -4.870   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      28.232  -4.100   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      29.566  -4.870   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      30.900  -4.100   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      32.233  -4.870   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      33.567  -4.100   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      33.567  -2.560   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      34.901  -4.870   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      36.234  -4.100   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9   10                                             
CONECT    8    7                                                            
CONECT    9    7                                                            
CONECT   10    7   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   37                                                  
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14   16   17                                                  
CONECT   16   15                                                            
CONECT   17   15   18                                                       
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   27                                                  
CONECT   22   21   23   24                                                  
CONECT   23   22                                                            
CONECT   24   22   25                                                       
CONECT   25   24   26   27                                                  
CONECT   26   25                                                            
CONECT   27   25   21   28                                                  
CONECT   28   27   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   32                                                  
CONECT   31   30                                                            
CONECT   32   30   33                                                       
CONECT   33   32   34                                                       
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35                                                            
CONECT   37   12   38                                                       
CONECT   38   37   39   40                                                  
CONECT   39   38                                                            
CONECT   40   38   41                                                       
CONECT   41   40   42                                                       
CONECT   42   41   43                                                       
CONECT   43   42   44                                                       
CONECT   44   43   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   58                                                  
CONECT   57   56                                                            
CONECT   58   56   59                                                       
CONECT   59   58                                                            
MASTER        0    0    0    0    0    0    0    0   59    0  118    0
END
Download

3D PDB for HMDB0270886 (PG(5-iso PGF2VI/a-21:0))

COMPND    HMDB0270886
HETATM    1  C1  UNL     1      15.024   2.034   0.030  1.00  0.00           C  
HETATM    2  C2  UNL     1      14.886   3.459   0.525  1.00  0.00           C  
HETATM    3  C3  UNL     1      13.533   4.027   0.243  1.00  0.00           C  
HETATM    4  C4  UNL     1      12.432   3.217   0.921  1.00  0.00           C  
HETATM    5  C5  UNL     1      11.072   3.806   0.616  1.00  0.00           C  
HETATM    6  C6  UNL     1      10.007   2.982   1.303  1.00  0.00           C  
HETATM    7  O1  UNL     1      10.209   2.987   2.671  1.00  0.00           O  
HETATM    8  C7  UNL     1       8.640   3.462   0.940  1.00  0.00           C  
HETATM    9  C8  UNL     1       8.204   3.505  -0.298  1.00  0.00           C  
HETATM   10  C9  UNL     1       6.860   3.971  -0.733  1.00  0.00           C  
HETATM   11  C10 UNL     1       6.225   3.023  -1.754  1.00  0.00           C  
HETATM   12  C11 UNL     1       5.811   1.739  -1.136  1.00  0.00           C  
HETATM   13  C12 UNL     1       5.206   0.755  -2.023  1.00  0.00           C  
HETATM   14  C13 UNL     1       3.976   0.324  -1.876  1.00  0.00           C  
HETATM   15  C14 UNL     1       3.104   0.806  -0.806  1.00  0.00           C  
HETATM   16  C15 UNL     1       2.650  -0.251   0.146  1.00  0.00           C  
HETATM   17  O2  UNL     1       1.486  -0.152   0.598  1.00  0.00           O  
HETATM   18  O3  UNL     1       3.427  -1.306   0.547  1.00  0.00           O  
HETATM   19  C16 UNL     1       3.106  -2.344   1.415  1.00  0.00           C  
HETATM   20  C17 UNL     1       2.049  -3.241   0.835  1.00  0.00           C  
HETATM   21  C18 UNL     1       2.636  -3.743  -0.501  1.00  0.00           C  
HETATM   22  O4  UNL     1       3.812  -4.417  -0.288  1.00  0.00           O  
HETATM   23  P1  UNL     1       4.436  -4.950  -1.756  1.00  0.00           P  
HETATM   24  O5  UNL     1       5.677  -4.118  -2.049  1.00  0.00           O  
HETATM   25  O6  UNL     1       3.285  -4.683  -2.957  1.00  0.00           O  
HETATM   26  O7  UNL     1       4.832  -6.576  -1.622  1.00  0.00           O  
HETATM   27  C19 UNL     1       4.708  -6.957  -0.291  1.00  0.00           C  
HETATM   28  C20 UNL     1       5.082  -8.432  -0.234  1.00  0.00           C  
HETATM   29  O8  UNL     1       4.998  -8.948   1.042  1.00  0.00           O  
HETATM   30  C21 UNL     1       4.145  -9.191  -1.145  1.00  0.00           C  
HETATM   31  O9  UNL     1       4.534 -10.547  -1.139  1.00  0.00           O  
HETATM   32  O10 UNL     1       0.879  -2.570   0.563  1.00  0.00           O  
HETATM   33  C22 UNL     1      -0.392  -2.870   1.028  1.00  0.00           C  
HETATM   34  O11 UNL     1      -0.506  -3.854   1.787  1.00  0.00           O  
HETATM   35  C23 UNL     1      -1.515  -2.032   0.610  1.00  0.00           C  
HETATM   36  C24 UNL     1      -1.901  -0.963   1.629  1.00  0.00           C  
HETATM   37  C25 UNL     1      -3.051  -0.161   1.117  1.00  0.00           C  
HETATM   38  C26 UNL     1      -4.304  -0.993   0.836  1.00  0.00           C  
HETATM   39  C27 UNL     1      -4.818  -1.640   2.052  1.00  0.00           C  
HETATM   40  C28 UNL     1      -5.948  -2.575   2.011  1.00  0.00           C  
HETATM   41  C29 UNL     1      -7.252  -2.165   1.440  1.00  0.00           C  
HETATM   42  C30 UNL     1      -7.276  -1.944  -0.012  1.00  0.00           C  
HETATM   43  C31 UNL     1      -8.650  -1.473  -0.537  1.00  0.00           C  
HETATM   44  C32 UNL     1      -9.660  -2.491  -0.218  1.00  0.00           C  
HETATM   45  C33 UNL     1     -11.031  -2.353  -0.726  1.00  0.00           C  
HETATM   46  C34 UNL     1     -11.883  -1.201  -0.422  1.00  0.00           C  
HETATM   47  C35 UNL     1     -11.488   0.130  -0.946  1.00  0.00           C  
HETATM   48  C36 UNL     1     -12.515   1.204  -0.544  1.00  0.00           C  
HETATM   49  C37 UNL     1     -12.100   2.538  -1.093  1.00  0.00           C  
HETATM   50  C38 UNL     1     -13.095   3.602  -0.708  1.00  0.00           C  
HETATM   51  C39 UNL     1     -13.245   3.777   0.781  1.00  0.00           C  
HETATM   52  C40 UNL     1     -14.272   4.873   1.005  1.00  0.00           C  
HETATM   53  C41 UNL     1     -11.908   4.269   1.334  1.00  0.00           C  
HETATM   54  C42 UNL     1     -12.010   4.463   2.829  1.00  0.00           C  
HETATM   55  C43 UNL     1       7.264   2.979  -2.808  1.00  0.00           C  
HETATM   56  O12 UNL     1       6.694   2.682  -4.055  1.00  0.00           O  
HETATM   57  C44 UNL     1       7.781   4.421  -2.849  1.00  0.00           C  
HETATM   58  C45 UNL     1       7.145   5.147  -1.681  1.00  0.00           C  
HETATM   59  O13 UNL     1       5.889   5.617  -2.068  1.00  0.00           O  
HETATM   60  H1  UNL     1      14.802   1.311   0.834  1.00  0.00           H  
HETATM   61  H2  UNL     1      14.287   1.887  -0.766  1.00  0.00           H  
HETATM   62  H3  UNL     1      16.066   1.891  -0.321  1.00  0.00           H  
HETATM   63  H4  UNL     1      15.036   3.483   1.633  1.00  0.00           H  
HETATM   64  H5  UNL     1      15.645   4.107   0.046  1.00  0.00           H  
HETATM   65  H6  UNL     1      13.329   4.110  -0.843  1.00  0.00           H  
HETATM   66  H7  UNL     1      13.487   5.040   0.666  1.00  0.00           H  
HETATM   67  H8  UNL     1      12.623   3.173   2.015  1.00  0.00           H  
HETATM   68  H9  UNL     1      12.495   2.186   0.513  1.00  0.00           H  
HETATM   69  H10 UNL     1      10.865   3.768  -0.473  1.00  0.00           H  
HETATM   70  H11 UNL     1      11.074   4.855   0.942  1.00  0.00           H  
HETATM   71  H12 UNL     1      10.120   1.942   0.944  1.00  0.00           H  
HETATM   72  H13 UNL     1      10.881   3.645   2.959  1.00  0.00           H  
HETATM   73  H14 UNL     1       7.977   3.790   1.729  1.00  0.00           H  
HETATM   74  H15 UNL     1       8.884   3.173  -1.074  1.00  0.00           H  
HETATM   75  H16 UNL     1       6.198   4.225   0.088  1.00  0.00           H  
HETATM   76  H17 UNL     1       5.363   3.612  -2.164  1.00  0.00           H  
HETATM   77  H18 UNL     1       5.310   1.950  -0.191  1.00  0.00           H  
HETATM   78  H19 UNL     1       6.804   1.258  -0.787  1.00  0.00           H  
HETATM   79  H20 UNL     1       5.816   0.349  -2.865  1.00  0.00           H  
HETATM   80  H21 UNL     1       3.566  -0.436  -2.586  1.00  0.00           H  
HETATM   81  H22 UNL     1       2.127   1.135  -1.319  1.00  0.00           H  
HETATM   82  H23 UNL     1       3.409   1.697  -0.267  1.00  0.00           H  
HETATM   83  H24 UNL     1       4.049  -2.932   1.610  1.00  0.00           H  
HETATM   84  H25 UNL     1       2.816  -1.980   2.433  1.00  0.00           H  
HETATM   85  H26 UNL     1       1.881  -4.133   1.506  1.00  0.00           H  
HETATM   86  H27 UNL     1       2.779  -2.856  -1.146  1.00  0.00           H  
HETATM   87  H28 UNL     1       1.841  -4.359  -0.987  1.00  0.00           H  
HETATM   88  H29 UNL     1       2.889  -5.581  -3.176  1.00  0.00           H  
HETATM   89  H30 UNL     1       3.655  -6.856   0.061  1.00  0.00           H  
HETATM   90  H31 UNL     1       5.414  -6.409   0.373  1.00  0.00           H  
HETATM   91  H32 UNL     1       6.115  -8.518  -0.654  1.00  0.00           H  
HETATM   92  H33 UNL     1       4.786  -8.184   1.655  1.00  0.00           H  
HETATM   93  H34 UNL     1       3.098  -9.108  -0.778  1.00  0.00           H  
HETATM   94  H35 UNL     1       4.234  -8.835  -2.191  1.00  0.00           H  
HETATM   95  H36 UNL     1       4.168 -11.016  -0.365  1.00  0.00           H  
HETATM   96  H37 UNL     1      -1.272  -1.478  -0.321  1.00  0.00           H  
HETATM   97  H38 UNL     1      -2.423  -2.620   0.388  1.00  0.00           H  
HETATM   98  H39 UNL     1      -2.115  -1.470   2.575  1.00  0.00           H  
HETATM   99  H40 UNL     1      -1.002  -0.283   1.730  1.00  0.00           H  
HETATM  100  H41 UNL     1      -2.796   0.364   0.190  1.00  0.00           H  
HETATM  101  H42 UNL     1      -3.351   0.612   1.857  1.00  0.00           H  
HETATM  102  H43 UNL     1      -5.042  -0.158   0.557  1.00  0.00           H  
HETATM  103  H44 UNL     1      -4.188  -1.641  -0.016  1.00  0.00           H  
HETATM  104  H45 UNL     1      -3.939  -2.188   2.546  1.00  0.00           H  
HETATM  105  H46 UNL     1      -5.061  -0.851   2.856  1.00  0.00           H  
HETATM  106  H47 UNL     1      -5.636  -3.515   1.437  1.00  0.00           H  
HETATM  107  H48 UNL     1      -6.167  -3.002   3.056  1.00  0.00           H  
HETATM  108  H49 UNL     1      -7.685  -1.278   1.994  1.00  0.00           H  
HETATM  109  H50 UNL     1      -7.963  -3.032   1.650  1.00  0.00           H  
HETATM  110  H51 UNL     1      -6.520  -1.288  -0.393  1.00  0.00           H  
HETATM  111  H52 UNL     1      -7.085  -2.947  -0.504  1.00  0.00           H  
HETATM  112  H53 UNL     1      -8.562  -1.303  -1.606  1.00  0.00           H  
HETATM  113  H54 UNL     1      -8.817  -0.520   0.057  1.00  0.00           H  
HETATM  114  H55 UNL     1      -9.729  -2.643   0.923  1.00  0.00           H  
HETATM  115  H56 UNL     1      -9.269  -3.490  -0.569  1.00  0.00           H  
HETATM  116  H57 UNL     1     -10.986  -2.499  -1.876  1.00  0.00           H  
HETATM  117  H58 UNL     1     -11.584  -3.315  -0.433  1.00  0.00           H  
HETATM  118  H59 UNL     1     -12.946  -1.430  -0.781  1.00  0.00           H  
HETATM  119  H60 UNL     1     -12.050  -1.138   0.701  1.00  0.00           H  
HETATM  120  H61 UNL     1     -11.538   0.107  -2.063  1.00  0.00           H  
HETATM  121  H62 UNL     1     -10.532   0.518  -0.656  1.00  0.00           H  
HETATM  122  H63 UNL     1     -12.504   1.248   0.565  1.00  0.00           H  
HETATM  123  H64 UNL     1     -13.508   0.887  -0.891  1.00  0.00           H  
HETATM  124  H65 UNL     1     -11.072   2.773  -0.755  1.00  0.00           H  
HETATM  125  H66 UNL     1     -12.118   2.456  -2.218  1.00  0.00           H  
HETATM  126  H67 UNL     1     -14.076   3.302  -1.171  1.00  0.00           H  
HETATM  127  H68 UNL     1     -12.818   4.569  -1.206  1.00  0.00           H  
HETATM  128  H69 UNL     1     -13.523   2.852   1.285  1.00  0.00           H  
HETATM  129  H70 UNL     1     -13.942   5.541   1.810  1.00  0.00           H  
HETATM  130  H71 UNL     1     -14.473   5.420   0.062  1.00  0.00           H  
HETATM  131  H72 UNL     1     -15.202   4.369   1.395  1.00  0.00           H  
HETATM  132  H73 UNL     1     -11.589   5.173   0.804  1.00  0.00           H  
HETATM  133  H74 UNL     1     -11.166   3.434   1.172  1.00  0.00           H  
HETATM  134  H75 UNL     1     -10.994   4.278   3.252  1.00  0.00           H  
HETATM  135  H76 UNL     1     -12.778   3.759   3.213  1.00  0.00           H  
HETATM  136  H77 UNL     1     -12.287   5.536   3.006  1.00  0.00           H  
HETATM  137  H78 UNL     1       8.072   2.251  -2.671  1.00  0.00           H  
HETATM  138  H79 UNL     1       5.818   3.102  -4.070  1.00  0.00           H  
HETATM  139  H80 UNL     1       8.863   4.485  -2.733  1.00  0.00           H  
HETATM  140  H81 UNL     1       7.520   4.926  -3.785  1.00  0.00           H  
HETATM  141  H82 UNL     1       7.778   5.905  -1.222  1.00  0.00           H  
HETATM  142  H83 UNL     1       5.482   6.176  -1.358  1.00  0.00           H  
CONECT    1    2   60   61   62
CONECT    2    3   63   64
CONECT    3    4   65   66
CONECT    4    5   67   68
CONECT    5    6   69   70
CONECT    6    7    8   71
CONECT    7   72
CONECT    8    9    9   73
CONECT    9   10   74
CONECT   10   11   58   75
CONECT   11   12   55   76
CONECT   12   13   77   78
CONECT   13   14   14   79
CONECT   14   15   80
CONECT   15   16   81   82
CONECT   16   17   17   18
CONECT   18   19
CONECT   19   20   83   84
CONECT   20   21   32   85
CONECT   21   22   86   87
CONECT   22   23
CONECT   23   24   24   25   26
CONECT   25   88
CONECT   26   27
CONECT   27   28   89   90
CONECT   28   29   30   91
CONECT   29   92
CONECT   30   31   93   94
CONECT   31   95
CONECT   32   33
CONECT   33   34   34   35
CONECT   35   36   96   97
CONECT   36   37   98   99
CONECT   37   38  100  101
CONECT   38   39  102  103
CONECT   39   40  104  105
CONECT   40   41  106  107
CONECT   41   42  108  109
CONECT   42   43  110  111
CONECT   43   44  112  113
CONECT   44   45  114  115
CONECT   45   46  116  117
CONECT   46   47  118  119
CONECT   47   48  120  121
CONECT   48   49  122  123
CONECT   49   50  124  125
CONECT   50   51  126  127
CONECT   51   52   53  128
CONECT   52  129  130  131
CONECT   53   54  132  133
CONECT   54  134  135  136
CONECT   55   56   57  137
CONECT   56  138
CONECT   57   58  139  140
CONECT   58   59  141
CONECT   59  142
END
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SMILES for HMDB0270886 (PG(5-iso PGF2VI/a-21:0))

CCCCC[C@@H](O)\C=C\[C@H]1[C@H](O)C[C@H](O)[C@H]1C\C=C/CC(=O)OC[C@H](COP(O)(=O)OC[C@@H](O)CO)OC(=O)CCCCCCCCCCCCCCCCC(C)CC
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INCHI for HMDB0270886 (PG(5-iso PGF2VI/a-21:0))

InChI=1S/C45H83O13P/c1-4-6-19-25-37(47)29-30-41-40(42(49)31-43(41)50)26-22-23-27-44(51)55-34-39(35-57-59(53,54)56-33-38(48)32-46)58-45(52)28-21-18-16-14-12-10-8-7-9-11-13-15-17-20-24-36(3)5-2/h22-23,29-30,36-43,46-50H,4-21,24-28,31-35H2,1-3H3,(H,53,54)/b23-22-,30-29+/t36?,37-,38+,39-,40+,41-,42+,43-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
[(2R)-3-{[(3Z)-5-[(1S,2R,3R,5S)-3,5-dihydroxy-2-[(1E,3R)-3-hydroxyoct-1-en-1-yl]cyclopentyl]pent-3-enoyl]oxy}-2-[(18-methylicosanoyl)oxy]propoxy][(2S)-2,3-dihydroxypropoxy]phosphinateHMDB
Chemical FormulaC45H83O13P
Average Molecular Weight863.12
Monoisotopic Molecular Weight862.557129731
IUPAC Name[(2R)-3-{[(3Z)-5-[(1S,2R,3R,5S)-3,5-dihydroxy-2-[(1E,3R)-3-hydroxyoct-1-en-1-yl]cyclopentyl]pent-3-enoyl]oxy}-2-[(18-methylicosanoyl)oxy]propoxy][(2S)-2,3-dihydroxypropoxy]phosphinic acid
Traditional Name(2R)-3-{[(3Z)-5-[(1S,2R,3R,5S)-3,5-dihydroxy-2-[(1E,3R)-3-hydroxyoct-1-en-1-yl]cyclopentyl]pent-3-enoyl]oxy}-2-[(18-methylicosanoyl)oxy]propoxy((2S)-2,3-dihydroxypropoxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
CCCCC[C@@H](O)\C=C\[C@H]1[C@H](O)C[C@H](O)[C@H]1C\C=C/CC(=O)OC[C@H](COP(O)(=O)OC[C@@H](O)CO)OC(=O)CCCCCCCCCCCCCCCCC(C)CC
InChI Identifier
InChI=1S/C45H83O13P/c1-4-6-19-25-37(47)29-30-41-40(42(49)31-43(41)50)26-22-23-27-44(51)55-34-39(35-57-59(53,54)56-33-38(48)32-46)58-45(52)28-21-18-16-14-12-10-8-7-9-11-13-15-17-20-24-36(3)5-2/h22-23,29-30,36-43,46-50H,4-21,24-28,31-35H2,1-3H3,(H,53,54)/b23-22-,30-29+/t36?,37-,38+,39-,40+,41-,42+,43-/m1/s1
InChI KeyOAOOSHIMLCCREY-KIVQXAQVSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as prostaglandins and related compounds. These are unsaturated carboxylic acids consisting of a 20 carbon skeleton that also contains a five member ring, and are based upon the fatty acid arachidonic acid.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassEicosanoids
Direct ParentProstaglandins and related compounds
Alternative Parents
Substituents
  • Prostaglandin skeleton
  • 1,2-diacylglycerophosphoglycerol
  • Glycerophospholipid
  • Dialkyl phosphate
  • Fatty acid ester
  • Alkyl phosphate
  • Phosphoric acid ester
  • Organic phosphoric acid derivative
  • Dicarboxylic acid or derivatives
  • Cyclopentanol
  • Cyclic alcohol
  • Secondary alcohol
  • Carboxylic acid ester
  • Carboxylic acid derivative
  • Organic oxygen compound
  • Organic oxide
  • Hydrocarbon derivative
  • Primary alcohol
  • Organooxygen compound
  • Carbonyl group
  • Alcohol
  • Aliphatic homomonocyclic compound
Molecular FrameworkAliphatic homomonocyclic compounds
External DescriptorsNot Available
Ontology
Physiological effectNot Available
Disposition
Source
ProcessNot Available
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
logP6.29ALOGPS
logP8.47ChemAxon
logS-6.3ALOGPS
pKa (Strongest Acidic)1.89ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge-1ChemAxon
Hydrogen Acceptor Count9ChemAxon
Hydrogen Donor Count6ChemAxon
Polar Surface Area209.51 ŲChemAxon
Rotatable Bond Count40ChemAxon
Refractivity232.45 m³·mol⁻¹ChemAxon
Polarizability101.34 ųChemAxon
Number of Rings1ChemAxon
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]+297.132859911
AllCCS[M+H-H2O]+297.24932859911
AllCCS[M+Na]+296.87232859911
AllCCS[M+NH4]+296.92832859911
AllCCS[M-H]-295.29632859911
AllCCS[M+Na-2H]-301.54632859911
AllCCS[M+HCOO]-308.42132859911
DeepCCS[M+H]+280.38130932474
DeepCCS[M-H]-278.65830932474
DeepCCS[M-2H]-313.12530932474
DeepCCS[M+Na]+287.03530932474

Predicted Kovats Retention Indices

Underivatized

MetaboliteSMILESKovats RI ValueColumn TypeReference
PG(5-iso PGF2VI/a-21:0)CCCCC[C@@H](O)\C=C\[C@H]1[C@H](O)C[C@H](O)[C@H]1C\C=C/CC(=O)OC[C@H](COP(O)(=O)OC[C@@H](O)CO)OC(=O)CCCCCCCCCCCCCCCCC(C)CC5297.5Standard polar33892256
PG(5-iso PGF2VI/a-21:0)CCCCC[C@@H](O)\C=C\[C@H]1[C@H](O)C[C@H](O)[C@H]1C\C=C/CC(=O)OC[C@H](COP(O)(=O)OC[C@@H](O)CO)OC(=O)CCCCCCCCCCCCCCCCC(C)CC4751.7Standard non polar33892256
PG(5-iso PGF2VI/a-21:0)CCCCC[C@@H](O)\C=C\[C@H]1[C@H](O)C[C@H](O)[C@H]1C\C=C/CC(=O)OC[C@H](COP(O)(=O)OC[C@@H](O)CO)OC(=O)CCCCCCCCCCCCCCCCC(C)CC6180.9Semi standard non polar33892256
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PG(5-iso PGF2VI/a-21:0) 10V, Negative-QTOFsplash10-03di-0000000090-fe56d1d773293a657ad02021-09-28Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PG(5-iso PGF2VI/a-21:0) 20V, Negative-QTOFsplash10-01t9-0009130040-a49b2afc14ca9d9b6e1b2021-09-28Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - PG(5-iso PGF2VI/a-21:0) 40V, Negative-QTOFsplash10-01t9-0109130040-544bf7ec90e1275407352021-09-28Wishart 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 Compound156974238
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General References
  1. Hajeyah AA, Griffiths WJ, Wang Y, Finch AJ, O'Donnell VB: The Biosynthesis of Enzymatically Oxidized Lipids. Front Endocrinol (Lausanne). 2020 Nov 19;11:591819. doi: 10.3389/fendo.2020.591819. eCollection 2020. [PubMed:33329396 ]