Hmdb loader

Showing metabocard for DG(13:0/0:0/PGD2) (HMDB0294875)

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IdentificationTaxonomyOntologyPhysical propertiesSpectraBiological propertiesConcentrationsLinksReferencesenzymes (131)transporters (1) Show 132 proteinsXML
enzymes (131)transporters (1) Show 132 proteins
Record Information
Version5.0
StatusPredicted
Creation Date2021-09-18 04:26:21 UTC
Update Date2022-11-30 20:09:13 UTC
HMDB IDHMDB0294875
Secondary Accession NumbersNone
Metabolite Identification
Common NameDG(13:0/0:0/PGD2)
DescriptionDG(13:0/0:0/PGD2) belongs to the family of Diacylglycerols. These are glycerolipids lipids containing a common glycerol backbone to which at least one fatty acyl group is esterified. It is involved in the phospholipid metabolic pathway.
Structure
Thumb
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0294875 (DG(13:0/0:0/PGD2))


  Mrv1652309182106262D          

 44 44  0  0  1  0            999 V2000
    7.1522  -16.5860    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4377  -16.9985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4377  -17.8235    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.7232  -16.5860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0087  -16.9985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2943  -16.5860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5798  -16.9985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8653  -16.5860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1509  -16.9985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4364  -16.5860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7219  -16.9985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0074  -16.5860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   -1.4215  -16.5860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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    7.8666  -16.9985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5811  -16.5860    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.2956  -16.9985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0100  -16.5860    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.7245  -16.9985    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   11.4390  -16.5860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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   14.2969  -16.5860    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

3D MOL for HMDB0294875 (DG(13:0/0:0/PGD2))

HMDB0294875
     RDKit          3D
DG(13:0/0:0/PGD2)
106106  0  0  0  0  0  0  0  0999 V2000
   13.6634    1.0358   -1.4649 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8061   -0.4347   -1.6774 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1092   -1.2175   -0.6062 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6223   -0.9116   -0.5621 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9747   -1.7291    0.5264 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4838   -1.4822    0.6121 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1113   -0.0710    0.9203 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6127    0.0805    0.9300 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9860   -0.7857    1.9585 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4987   -0.6907    1.9663 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0405    0.7073    2.2643 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4870    0.6644    2.1957 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.1517    0.2323    0.7992 C   0  0  0  0  0  0  0  0  0  0  0  0
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 44106  1  0
M  END
Download

3D SDF for HMDB0294875 (DG(13:0/0:0/PGD2))


  Mrv1652309182106262D          

 44 44  0  0  1  0            999 V2000
    7.1522  -16.5860    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
> <DATABASE_ID>
HMDB0294875

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCCCCCCCCC(=O)OC[C@@H](O)COC(=O)CCC\C=C/C[C@H]1[C@@H](O)CC(=O)[C@@H]1\C=C\[C@@H](O)CCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C36H62O8/c1-3-5-7-8-9-10-11-12-13-18-22-35(41)43-27-30(38)28-44-36(42)23-19-15-14-17-21-31-32(34(40)26-33(31)39)25-24-29(37)20-16-6-4-2/h14,17,24-25,29-33,37-39H,3-13,15-16,18-23,26-28H2,1-2H3/b17-14-,25-24+/t29-,30+,31+,32+,33-/m0/s1

> <INCHI_KEY>
OKRPYNXLXZTXTF-NHRNMUDESA-N

> <FORMULA>
C36H62O8

> <MOLECULAR_WEIGHT>
622.884

> <EXACT_MASS>
622.444468956

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
106

> <JCHEM_AVERAGE_POLARIZABILITY>
75.59618166506468

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2-hydroxy-3-{[(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoyl]oxy}propyl tridecanoate

> <ALOGPS_LOGP>
6.61

> <JCHEM_LOGP>
7.638075146333331

> <ALOGPS_LOGS>
-5.83

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
14.131350673534545

> <JCHEM_PKA_STRONGEST_ACIDIC>
13.471376523511005

> <JCHEM_PKA_STRONGEST_BASIC>
-1.5973943340377592

> <JCHEM_POLAR_SURFACE_AREA>
130.36

> <JCHEM_REFRACTIVITY>
176.24740000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
29

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
9.20e-04 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2-hydroxy-3-{[(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoyl]oxy}propyl tridecanoate

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0294875 (DG(13:0/0:0/PGD2))

HMDB0294875
     RDKit          3D
DG(13:0/0:0/PGD2)
106106  0  0  0  0  0  0  0  0999 V2000
   13.6634    1.0358   -1.4649 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.8061   -0.4347   -1.6774 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.1092   -1.2175   -0.6062 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.6223   -0.9116   -0.5621 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.9747   -1.7291    0.5264 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.4838   -1.4822    0.6121 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1113   -0.0710    0.9203 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6127    0.0805    0.9300 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9860   -0.7857    1.9585 C   0  0  0  0  0  0  0  0  0  0  0  0
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    5.0405    0.7073    2.2643 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4870    0.6644    2.1957 C   0  0  0  0  0  0  0  0  0  0  0  0
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  -12.3738    0.9195    0.0468 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.2874    2.0981    0.7586 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.5444    0.2613    2.1323 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8745    0.1084    1.6639 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8076   -2.0046    1.6399 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2664   -1.4987    0.7552 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.4278   -3.0170   -0.3508 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6974   -1.4983   -0.9079 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3816   -1.8291   -1.3308 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  2  0
 13 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 17 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  2  0
 21 23  1  0
 23 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  2  0
 27 28  1  0
 28 29  1  0
 29 30  1  0
 30 31  1  0
 30 32  1  0
 32 33  1  0
 33 34  2  0
 33 35  1  0
 35 36  1  0
 36 37  2  0
 37 38  1  0
 38 39  1  0
 38 40  1  0
 40 41  1  0
 41 42  1  0
 42 43  1  0
 43 44  1  0
 35 29  1  0
  1 45  1  0
  1 46  1  0
  1 47  1  0
  2 48  1  0
  2 49  1  0
  3 50  1  0
  3 51  1  0
  4 52  1  0
  4 53  1  0
  5 54  1  0
  5 55  1  0
  6 56  1  0
  6 57  1  0
  7 58  1  0
  7 59  1  0
  8 60  1  0
  8 61  1  0
  9 62  1  0
  9 63  1  0
 10 64  1  0
 10 65  1  0
 11 66  1  0
 11 67  1  0
 12 68  1  0
 12 69  1  0
 16 70  1  0
 16 71  1  0
 17 72  1  6
 18 73  1  0
 19 74  1  0
 19 75  1  0
 23 76  1  0
 23 77  1  0
 24 78  1  0
 24 79  1  0
 25 80  1  0
 25 81  1  0
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 28 84  1  0
 28 85  1  0
 29 86  1  6
 30 87  1  6
 31 88  1  0
 32 89  1  0
 32 90  1  0
 35 91  1  1
 36 92  1  0
 37 93  1  0
 38 94  1  1
 39 95  1  0
 40 96  1  0
 40 97  1  0
 41 98  1  0
 41 99  1  0
 42100  1  0
 42101  1  0
 43102  1  0
 43103  1  0
 44104  1  0
 44105  1  0
 44106  1  0
M  END
Download

PDB for HMDB0294875 (DG(13:0/0:0/PGD2))

HEADER    PROTEIN                                 18-SEP-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   18-SEP-21         0                                  
HETATM    1  O   UNK     0      13.351 -30.960   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      12.017 -31.730   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      12.017 -33.270   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      10.683 -30.960   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       9.350 -31.730   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       8.016 -30.960   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.682 -31.730   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.349 -30.960   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       4.015 -31.730   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.681 -30.960   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       1.348 -31.730   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0       0.014 -30.960   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -1.320 -31.730   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      -2.653 -30.960   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      -3.987 -31.730   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      14.684 -31.730   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      16.018 -30.960   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      17.352 -31.730   0.000  0.00  0.00           C+0
HETATM   19  O   UNK     0      18.685 -30.960   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      20.019 -31.730   0.000  0.00  0.00           C+0
HETATM   21  O   UNK     0      20.019 -33.270   0.000  0.00  0.00           O+0
HETATM   22  C   UNK     0      21.353 -30.960   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      22.686 -31.730   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      24.020 -30.960   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      25.354 -31.730   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      26.687 -30.960   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      26.687 -29.420   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      28.021 -28.650   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      28.182 -27.119   0.000  0.00  0.00           C+0
HETATM   30  O   UNK     0      27.038 -26.088   0.000  0.00  0.00           O+0
HETATM   31  C   UNK     0      29.688 -26.799   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      30.458 -28.132   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      31.990 -28.293   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      29.428 -29.277   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0      29.748 -30.783   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0      28.604 -31.814   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      28.924 -33.320   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0      27.779 -34.350   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0      30.389 -33.796   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0      30.709 -35.302   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0      32.173 -35.778   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0      32.494 -37.284   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0      33.958 -37.760   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      16.018 -29.420   0.000  0.00  0.00           O+0
CONECT    1    2   16                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13                                                       
CONECT   13   12   14                                                       
CONECT   14   13   15                                                       
CONECT   15   14                                                            
CONECT   16    1   17                                                       
CONECT   17   16   18   44                                                  
CONECT   18   17   19                                                       
CONECT   19   18   20                                                       
CONECT   20   19   21   22                                                  
CONECT   21   20                                                            
CONECT   22   20   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   34                                                  
CONECT   29   28   30   31                                                  
CONECT   30   29                                                            
CONECT   31   29   32                                                       
CONECT   32   31   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   28   35                                                  
CONECT   35   34   36                                                       
CONECT   36   35   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                                                            
CONECT   44   17                                                            
MASTER        0    0    0    0    0    0    0    0   44    0   88    0
END
Download

3D PDB for HMDB0294875 (DG(13:0/0:0/PGD2))

COMPND    HMDB0294875
HETATM    1  C1  UNL     1      13.663   1.036  -1.465  1.00  0.00           C  
HETATM    2  C2  UNL     1      13.806  -0.435  -1.677  1.00  0.00           C  
HETATM    3  C3  UNL     1      13.109  -1.218  -0.606  1.00  0.00           C  
HETATM    4  C4  UNL     1      11.622  -0.912  -0.562  1.00  0.00           C  
HETATM    5  C5  UNL     1      10.975  -1.729   0.526  1.00  0.00           C  
HETATM    6  C6  UNL     1       9.484  -1.482   0.612  1.00  0.00           C  
HETATM    7  C7  UNL     1       9.111  -0.071   0.920  1.00  0.00           C  
HETATM    8  C8  UNL     1       7.613   0.080   0.930  1.00  0.00           C  
HETATM    9  C9  UNL     1       6.986  -0.786   1.959  1.00  0.00           C  
HETATM   10  C10 UNL     1       5.499  -0.691   1.966  1.00  0.00           C  
HETATM   11  C11 UNL     1       5.041   0.707   2.264  1.00  0.00           C  
HETATM   12  C12 UNL     1       3.487   0.664   2.196  1.00  0.00           C  
HETATM   13  C13 UNL     1       3.152   0.232   0.799  1.00  0.00           C  
HETATM   14  O1  UNL     1       3.329   1.069  -0.134  1.00  0.00           O  
HETATM   15  O2  UNL     1       2.670  -1.017   0.489  1.00  0.00           O  
HETATM   16  C14 UNL     1       2.390  -1.381  -0.836  1.00  0.00           C  
HETATM   17  C15 UNL     1       1.357  -0.557  -1.522  1.00  0.00           C  
HETATM   18  O3  UNL     1       1.272  -1.030  -2.868  1.00  0.00           O  
HETATM   19  C16 UNL     1      -0.051  -0.780  -0.987  1.00  0.00           C  
HETATM   20  O4  UNL     1      -0.921  -0.003  -1.783  1.00  0.00           O  
HETATM   21  C17 UNL     1      -0.854   1.363  -1.750  1.00  0.00           C  
HETATM   22  O5  UNL     1      -0.031   1.936  -1.000  1.00  0.00           O  
HETATM   23  C18 UNL     1      -1.740   2.185  -2.588  1.00  0.00           C  
HETATM   24  C19 UNL     1      -2.513   3.135  -1.745  1.00  0.00           C  
HETATM   25  C20 UNL     1      -3.451   2.517  -0.755  1.00  0.00           C  
HETATM   26  C21 UNL     1      -2.888   1.638   0.242  1.00  0.00           C  
HETATM   27  C22 UNL     1      -3.229   0.371   0.344  1.00  0.00           C  
HETATM   28  C23 UNL     1      -4.201  -0.224  -0.554  1.00  0.00           C  
HETATM   29  C24 UNL     1      -5.448  -0.793   0.102  1.00  0.00           C  
HETATM   30  C25 UNL     1      -5.208  -1.891   1.062  1.00  0.00           C  
HETATM   31  O6  UNL     1      -3.907  -2.162   1.396  1.00  0.00           O  
HETATM   32  C26 UNL     1      -6.070  -1.619   2.282  1.00  0.00           C  
HETATM   33  C27 UNL     1      -6.467  -0.208   2.172  1.00  0.00           C  
HETATM   34  O7  UNL     1      -6.921   0.447   3.105  1.00  0.00           O  
HETATM   35  C28 UNL     1      -6.237   0.257   0.813  1.00  0.00           C  
HETATM   36  C29 UNL     1      -7.596   0.408   0.164  1.00  0.00           C  
HETATM   37  C30 UNL     1      -8.058   1.494  -0.363  1.00  0.00           C  
HETATM   38  C31 UNL     1      -9.253   1.908  -1.017  1.00  0.00           C  
HETATM   39  O8  UNL     1      -8.873   2.143  -2.415  1.00  0.00           O  
HETATM   40  C32 UNL     1     -10.567   1.278  -1.047  1.00  0.00           C  
HETATM   41  C33 UNL     1     -11.251   1.076   0.226  1.00  0.00           C  
HETATM   42  C34 UNL     1     -10.853   0.047   1.200  1.00  0.00           C  
HETATM   43  C35 UNL     1     -11.138  -1.353   0.764  1.00  0.00           C  
HETATM   44  C36 UNL     1     -10.606  -1.889  -0.487  1.00  0.00           C  
HETATM   45  H1  UNL     1      13.282   1.304  -0.461  1.00  0.00           H  
HETATM   46  H2  UNL     1      14.692   1.477  -1.520  1.00  0.00           H  
HETATM   47  H3  UNL     1      13.094   1.501  -2.297  1.00  0.00           H  
HETATM   48  H4  UNL     1      14.877  -0.756  -1.715  1.00  0.00           H  
HETATM   49  H5  UNL     1      13.342  -0.705  -2.657  1.00  0.00           H  
HETATM   50  H6  UNL     1      13.510  -0.898   0.391  1.00  0.00           H  
HETATM   51  H7  UNL     1      13.238  -2.302  -0.730  1.00  0.00           H  
HETATM   52  H8  UNL     1      11.437   0.155  -0.356  1.00  0.00           H  
HETATM   53  H9  UNL     1      11.116  -1.185  -1.512  1.00  0.00           H  
HETATM   54  H10 UNL     1      11.086  -2.817   0.308  1.00  0.00           H  
HETATM   55  H11 UNL     1      11.462  -1.502   1.510  1.00  0.00           H  
HETATM   56  H12 UNL     1       9.044  -1.794  -0.343  1.00  0.00           H  
HETATM   57  H13 UNL     1       9.122  -2.190   1.418  1.00  0.00           H  
HETATM   58  H14 UNL     1       9.462   0.243   1.927  1.00  0.00           H  
HETATM   59  H15 UNL     1       9.583   0.655   0.218  1.00  0.00           H  
HETATM   60  H16 UNL     1       7.320   1.149   1.075  1.00  0.00           H  
HETATM   61  H17 UNL     1       7.203  -0.243  -0.070  1.00  0.00           H  
HETATM   62  H18 UNL     1       7.341  -0.491   2.982  1.00  0.00           H  
HETATM   63  H19 UNL     1       7.248  -1.874   1.846  1.00  0.00           H  
HETATM   64  H20 UNL     1       5.073  -1.360   2.751  1.00  0.00           H  
HETATM   65  H21 UNL     1       5.092  -0.992   0.962  1.00  0.00           H  
HETATM   66  H22 UNL     1       5.374   1.052   3.249  1.00  0.00           H  
HETATM   67  H23 UNL     1       5.396   1.391   1.467  1.00  0.00           H  
HETATM   68  H24 UNL     1       3.131   1.682   2.375  1.00  0.00           H  
HETATM   69  H25 UNL     1       3.102  -0.046   2.939  1.00  0.00           H  
HETATM   70  H26 UNL     1       3.301  -1.409  -1.477  1.00  0.00           H  
HETATM   71  H27 UNL     1       1.999  -2.443  -0.778  1.00  0.00           H  
HETATM   72  H28 UNL     1       1.630   0.489  -1.602  1.00  0.00           H  
HETATM   73  H29 UNL     1       0.920  -1.954  -2.762  1.00  0.00           H  
HETATM   74  H30 UNL     1      -0.357  -1.835  -1.071  1.00  0.00           H  
HETATM   75  H31 UNL     1      -0.148  -0.395   0.060  1.00  0.00           H  
HETATM   76  H32 UNL     1      -2.419   1.532  -3.194  1.00  0.00           H  
HETATM   77  H33 UNL     1      -1.140   2.780  -3.342  1.00  0.00           H  
HETATM   78  H34 UNL     1      -3.152   3.789  -2.408  1.00  0.00           H  
HETATM   79  H35 UNL     1      -1.864   3.846  -1.186  1.00  0.00           H  
HETATM   80  H36 UNL     1      -3.832   3.431  -0.154  1.00  0.00           H  
HETATM   81  H37 UNL     1      -4.383   2.198  -1.260  1.00  0.00           H  
HETATM   82  H38 UNL     1      -2.149   2.047   0.937  1.00  0.00           H  
HETATM   83  H39 UNL     1      -2.753  -0.244   1.132  1.00  0.00           H  
HETATM   84  H40 UNL     1      -3.682  -1.186  -0.934  1.00  0.00           H  
HETATM   85  H41 UNL     1      -4.421   0.288  -1.492  1.00  0.00           H  
HETATM   86  H42 UNL     1      -6.083  -1.197  -0.724  1.00  0.00           H  
HETATM   87  H43 UNL     1      -5.623  -2.872   0.653  1.00  0.00           H  
HETATM   88  H44 UNL     1      -3.917  -2.833   2.121  1.00  0.00           H  
HETATM   89  H45 UNL     1      -6.991  -2.237   2.310  1.00  0.00           H  
HETATM   90  H46 UNL     1      -5.508  -1.867   3.219  1.00  0.00           H  
HETATM   91  H47 UNL     1      -5.768   1.264   0.755  1.00  0.00           H  
HETATM   92  H48 UNL     1      -8.189  -0.472   0.169  1.00  0.00           H  
HETATM   93  H49 UNL     1      -7.274   2.346  -0.271  1.00  0.00           H  
HETATM   94  H50 UNL     1      -9.430   3.055  -0.741  1.00  0.00           H  
HETATM   95  H51 UNL     1      -8.060   2.708  -2.378  1.00  0.00           H  
HETATM   96  H52 UNL     1     -10.635   0.397  -1.754  1.00  0.00           H  
HETATM   97  H53 UNL     1     -11.271   2.014  -1.633  1.00  0.00           H  
HETATM   98  H54 UNL     1     -12.374   0.920   0.047  1.00  0.00           H  
HETATM   99  H55 UNL     1     -11.287   2.098   0.759  1.00  0.00           H  
HETATM  100  H56 UNL     1     -11.544   0.261   2.132  1.00  0.00           H  
HETATM  101  H57 UNL     1      -9.875   0.108   1.664  1.00  0.00           H  
HETATM  102  H58 UNL     1     -10.808  -2.005   1.640  1.00  0.00           H  
HETATM  103  H59 UNL     1     -12.266  -1.499   0.755  1.00  0.00           H  
HETATM  104  H60 UNL     1     -10.428  -3.017  -0.351  1.00  0.00           H  
HETATM  105  H61 UNL     1      -9.697  -1.498  -0.908  1.00  0.00           H  
HETATM  106  H62 UNL     1     -11.382  -1.829  -1.331  1.00  0.00           H  
CONECT    1    2   45   46   47
CONECT    2    3   48   49
CONECT    3    4   50   51
CONECT    4    5   52   53
CONECT    5    6   54   55
CONECT    6    7   56   57
CONECT    7    8   58   59
CONECT    8    9   60   61
CONECT    9   10   62   63
CONECT   10   11   64   65
CONECT   11   12   66   67
CONECT   12   13   68   69
CONECT   13   14   14   15
CONECT   15   16
CONECT   16   17   70   71
CONECT   17   18   19   72
CONECT   18   73
CONECT   19   20   74   75
CONECT   20   21
CONECT   21   22   22   23
CONECT   23   24   76   77
CONECT   24   25   78   79
CONECT   25   26   80   81
CONECT   26   27   27   82
CONECT   27   28   83
CONECT   28   29   84   85
CONECT   29   30   35   86
CONECT   30   31   32   87
CONECT   31   88
CONECT   32   33   89   90
CONECT   33   34   34   35
CONECT   35   36   91
CONECT   36   37   37   92
CONECT   37   38   93
CONECT   38   39   40   94
CONECT   39   95
CONECT   40   41   96   97
CONECT   41   42   98   99
CONECT   42   43  100  101
CONECT   43   44  102  103
CONECT   44  104  105  106
END
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SMILES for HMDB0294875 (DG(13:0/0:0/PGD2))

CCCCCCCCCCCCC(=O)OC[C@@H](O)COC(=O)CCC\C=C/C[C@H]1[C@@H](O)CC(=O)[C@@H]1\C=C\[C@@H](O)CCCCC
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INCHI for HMDB0294875 (DG(13:0/0:0/PGD2))

InChI=1S/C36H62O8/c1-3-5-7-8-9-10-11-12-13-18-22-35(41)43-27-30(38)28-44-36(42)23-19-15-14-17-21-31-32(34(40)26-33(31)39)25-24-29(37)20-16-6-4-2/h14,17,24-25,29-33,37-39H,3-13,15-16,18-23,26-28H2,1-2H3/b17-14-,25-24+/t29-,30+,31+,32+,33-/m0/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
(2R)-2-Hydroxy-3-{[(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoyl]oxy}propyl tridecanoic acidGenerator
Chemical FormulaC36H62O8
Average Molecular Weight622.884
Monoisotopic Molecular Weight622.444468956
IUPAC Name(2R)-2-hydroxy-3-{[(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoyl]oxy}propyl tridecanoate
Traditional Name(2R)-2-hydroxy-3-{[(5Z)-7-[(1R,2R,5S)-5-hydroxy-2-[(1E,3S)-3-hydroxyoct-1-en-1-yl]-3-oxocyclopentyl]hept-5-enoyl]oxy}propyl tridecanoate
CAS Registry NumberNot Available
SMILES
CCCCCCCCCCCCC(=O)OC[C@@H](O)COC(=O)CCC\C=C/C[C@H]1[C@@H](O)CC(=O)[C@@H]1\C=C\[C@@H](O)CCCCC
InChI Identifier
InChI=1S/C36H62O8/c1-3-5-7-8-9-10-11-12-13-18-22-35(41)43-27-30(38)28-44-36(42)23-19-15-14-17-21-31-32(34(40)26-33(31)39)25-24-29(37)20-16-6-4-2/h14,17,24-25,29-33,37-39H,3-13,15-16,18-23,26-28H2,1-2H3/b17-14-,25-24+/t29-,30+,31+,32+,33-/m0/s1
InChI KeyOKRPYNXLXZTXTF-NHRNMUDESA-N
Chemical Taxonomy
ClassificationNot classified
Ontology
Physiological effectNot Available
DispositionNot Available
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
logP6.61ALOGPS
logP7.64ChemAxon
logS-5.8ALOGPS
pKa (Strongest Acidic)13.47ChemAxon
pKa (Strongest Basic)-1.6ChemAxon
Physiological Charge0ChemAxon
Hydrogen Acceptor Count6ChemAxon
Hydrogen Donor Count3ChemAxon
Polar Surface Area130.36 ŲChemAxon
Rotatable Bond Count29ChemAxon
Refractivity176.25 m³·mol⁻¹ChemAxon
Polarizability75.6 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]+256.932859911
AllCCS[M+H-H2O]+256.38632859911
AllCCS[M+Na]+257.46132859911
AllCCS[M+NH4]+257.34132859911
AllCCS[M-H]-245.26532859911
AllCCS[M+Na-2H]-250.08432859911
AllCCS[M+HCOO]-255.48532859911
DeepCCS[M+H]+250.30730932474
DeepCCS[M-H]-248.48230932474
DeepCCS[M-2H]-281.72330932474
DeepCCS[M+Na]+255.91330932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - DG(13:0/0:0/PGD2) 10V, Positive-QTOFsplash10-052r-0100095000-791e5c6c190de73f87d32021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - DG(13:0/0:0/PGD2) 20V, Positive-QTOFsplash10-0a4r-2217971000-80d38bf3883a6c049c6c2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - DG(13:0/0:0/PGD2) 40V, Positive-QTOFsplash10-0avi-9313100000-2fce90717881aa7ddbdb2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - DG(13:0/0:0/PGD2) 10V, Negative-QTOFsplash10-0zgr-2049317000-21bed2885a3ee7baa4242021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - DG(13:0/0:0/PGD2) 20V, Negative-QTOFsplash10-0f8c-3029101000-4c96cc514cc179d3cc9b2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - DG(13:0/0:0/PGD2) 40V, Negative-QTOFsplash10-11c1-5955000000-7d2afecc7eedd3955b322021-10-21Wishart 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 CompoundNot Available
PDB IDNot Available
ChEBI IDNot Available
Food Biomarker OntologyNot Available
VMH IDNot Available
MarkerDB IDNot Available
Good Scents IDNot Available
References
Synthesis ReferenceNot Available
Material Safety Data Sheet (MSDS)Not Available
General ReferencesNot Available

Only showing the first 10 proteins. There are 132 proteins in total.

Show all enzymes and transporters

Enzymes

Enzyme Details
1. Diacylglycerol kinase theta
General function:
Involved in diacylglycerol kinase activity
Specific function:
Phosphorylates diacylglycerol (DAG) to generate phosphatidic acid (PA). May regulate the activity of protein kinase C by controlling the balance between these two signaling lipids. Activated in the nucleus in response to alpha-thrombin and nerve growth factor. May be involved in cAMP- induced activation of NR5A1 and subsequent steroidogenic gene transcription by delivering PA as ligand for NR5A1. Acts synergistically with NR5A1 on CYP17 transcriptional activity
Gene Name:
DGKQ
Uniprot ID:
P52824
Molecular weight:
101154.0
Enzyme Details
2. Pancreatic triacylglycerol lipase
General function:
Involved in catalytic activity
Specific function:
Not Available
Gene Name:
PNLIP
Uniprot ID:
P16233
Molecular weight:
51156.48
Enzyme Details
3. 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1
General function:
Involved in calcium ion binding
Specific function:
The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes.
Gene Name:
PLCB1
Uniprot ID:
Q9NQ66
Molecular weight:
138565.805
Enzyme Details
4. 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-4
General function:
Involved in calcium ion binding
Specific function:
The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes. This form has a role in retina signal transduction.
Gene Name:
PLCB4
Uniprot ID:
Q15147
Molecular weight:
136105.065
Enzyme Details
5. 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2
General function:
Involved in calcium ion binding
Specific function:
The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes.
Gene Name:
PLCB2
Uniprot ID:
Q00722
Molecular weight:
134023.21
Enzyme Details
6. Diacylglycerol kinase gamma
General function:
Involved in diacylglycerol kinase activity
Specific function:
Reverses the normal flow of glycerolipid biosynthesis by phosphorylating diacylglycerol back to phosphatidic acid
Gene Name:
DGKG
Uniprot ID:
P49619
Molecular weight:
89095.3
Enzyme Details
7. Hepatic triacylglycerol lipase
General function:
Involved in catalytic activity
Specific function:
Hepatic lipase has the capacity to catalyze hydrolysis of phospholipids, mono-, di-, and triglycerides, and acyl-CoA thioesters. It is an important enzyme in HDL metabolism. Hepatic lipase binds heparin.
Gene Name:
LIPC
Uniprot ID:
P11150
Molecular weight:
55914.1
Enzyme Details
8. Lysosomal acid lipase/cholesteryl ester hydrolase
General function:
Involved in lipid metabolic process
Specific function:
Crucial for the intracellular hydrolysis of cholesteryl esters and triglycerides that have been internalized via receptor-mediated endocytosis of lipoprotein particles. Important in mediating the effect of LDL (low density lipoprotein) uptake on suppression of hydroxymethylglutaryl-CoA reductase and activation of endogenous cellular cholesteryl ester formation.
Gene Name:
LIPA
Uniprot ID:
P38571
Molecular weight:
45418.71
Enzyme Details
9. 1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-3
General function:
Involved in calcium ion binding
Specific function:
The production of the second messenger molecules diacylglycerol (DAG) and inositol 1,4,5-trisphosphate (IP3) is mediated by activated phosphatidylinositol-specific phospholipase C enzymes.
Gene Name:
PLCB3
Uniprot ID:
Q01970
Molecular weight:
138797.725
Enzyme Details
10. Inactive pancreatic lipase-related protein 1
General function:
Involved in catalytic activity
Specific function:
May function as inhibitor of dietary triglyceride digestion. Lacks detectable lipase activity towards triglycerides, diglycerides, phosphatidylcholine, galactolipids or cholesterol esters (in vitro) (By similarity).
Gene Name:
PNLIPRP1
Uniprot ID:
P54315
Molecular weight:
Not Available

Transporters

Enzyme Details
1. Long-chain fatty acid transport protein 1
General function:
Lipid transport and metabolism
Specific function:
Involved in translocation of long-chain fatty acids (LFCA) across the plasma membrane. The LFCA import appears to be hormone-regulated in a tissue-specific manner. In adipocytes, but not myocytes, insulin induces a rapid translocation of FATP1 from intracellular compartments to the plasma membrane, paralleled by increased LFCA uptake. May act directly as a bona fide transporter, or alternatively, in a cytoplasmic or membrane- associated multimeric protein complex to trap and draw fatty acids towards accumulation. Plays a pivotal role in regulating available LFCA substrates from exogenous sources in tissues undergoing high levels of beta-oxidation or triglyceride synthesis. May be involved in regulation of cholesterol metabolism. Has acyl-CoA ligase activity for long-chain and very-long-chain fatty acids
Gene Name:
SLC27A1
Uniprot ID:
Q6PCB7
Molecular weight:
71107.5

Only showing the first 10 proteins. There are 132 proteins in total.

Show all enzymes and transporters