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Showing metabocard for CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)) (HMDB0292513)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-17 07:54:47 UTC
Update Date2022-11-30 20:08:08 UTC
HMDB IDHMDB0292513
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17))
DescriptionCDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)) is an oxidized CDP-diacylglycerol (CDP-DG). Oxidized CDP-diacylglycerols are glycerophospholipids in which a cytidine diphosphate moiety occupies a glycerol substitution site and at least one of the fatty acyl chains has undergone oxidation. As all oxidized lipids, oxidized CDP-diacylglycerols 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, CDP-diacylglycerols 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. CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)), in particular, consists of one chain of one 4Z,7Z,10Z,13Z,16Z-docosapentaenoyl at the C-1 position and one chain of 16,17-epoxy-docosapentaenoyl 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 CDP-DGs can be synthesized via three different routes. In one route, the oxidized CDP-DG is synthetized de novo following the same mechanisms as for CDP-DGs 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 CDP-DG backbone, mainly through the action of LOX (PMID: 33329396 ).
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0292513 (CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)))

CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17))
  Mrv1652309172109552D          

 78 80  0  0  1  0            999 V2000
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M  END
Download

3D MOL for HMDB0292513 (CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)))

HMDB0292513
     RDKit          3D
CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17))
160162  0  0  0  0  0  0  0  0999 V2000
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M  END
Download

3D SDF for HMDB0292513 (CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)))

CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17))
  Mrv1652309172109552D          

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M  END
> <DATABASE_ID>
HMDB0292513

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](COC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)OC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/CC1OC1C\C=C/CC

> <INCHI_IDENTIFIER>
InChI=1S/C56H83N3O16P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-22-25-28-31-35-39-51(60)69-43-46(72-52(61)40-36-32-29-26-23-20-19-21-24-27-30-34-38-48-47(73-48)37-33-6-4-2)44-70-76(65,66)75-77(67,68)71-45-49-53(62)54(63)55(74-49)59-42-41-50(57)58-56(59)64/h6,9-10,12-13,15-16,18,20-24,28-34,41-42,46-49,53-55,62-63H,3-5,7-8,11,14,17,19,25-27,35-40,43-45H2,1-2H3,(H,65,66)(H,67,68)(H2,57,58,64)/b10-9-,13-12-,16-15-,22-18-,23-20-,24-21-,31-28-,32-29-,33-6-,34-30-/t46-,47?,48?,49-,53-,54-,55-/m1/s1

> <INCHI_KEY>
DMZKNSXMKRALSL-OKRMPEIJSA-N

> <FORMULA>
C56H83N3O16P2

> <MOLECULAR_WEIGHT>
1116.233

> <EXACT_MASS>
1115.524857601

> <JCHEM_ACCEPTOR_COUNT>
13

> <JCHEM_ATOM_COUNT>
160

> <JCHEM_AVERAGE_POLARIZABILITY>
116.57814511556421

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2R)-3-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-2-{[(4Z,7Z,10Z,13Z)-15-{3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}pentadeca-4,7,10,13-tetraenoyl]oxy}propoxy](hydroxy)phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
7.01

> <JCHEM_LOGP>
9.972438630333333

> <ALOGPS_LOGS>
-5.86

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
3.27162556801157

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.863167720698256

> <JCHEM_PKA_STRONGEST_BASIC>
-0.031961291817737436

> <JCHEM_POLAR_SURFACE_AREA>
275.8

> <JCHEM_REFRACTIVITY>
306.1093999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
43

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.53e-03 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([(2R)-3-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-2-{[(4Z,7Z,10Z,13Z)-15-{3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}pentadeca-4,7,10,13-tetraenoyl]oxy}propoxy(hydroxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0292513 (CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)))

HMDB0292513
     RDKit          3D
CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17))
160162  0  0  0  0  0  0  0  0999 V2000
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M  END
Download

PDB for HMDB0292513 (CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)))

HEADER    PROTEIN                                 17-SEP-21   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-SEP-21         0                                  
HETATM    1  O   UNK     0      -7.097   0.673   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -5.781   1.440   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -4.447   0.670   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -3.113   1.440   0.000  0.00  0.00           C+0
HETATM    5  H   UNK     0      -3.677  -0.663   0.000  0.00  0.00           H+0
HETATM    6  O   UNK     0      -5.217  -0.663   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       9.112  -2.009   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       5.770  -1.994   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       4.894   1.462   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       3.559   0.694   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0       2.225   1.462   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0       0.890   0.694   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0      -0.456   1.444   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0      -1.790   0.671   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.290   2.790   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -1.251   2.763   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       2.997   2.801   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0       1.456   2.801   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      11.394  -0.846   0.000  0.00  0.00           O+0
HETATM   20  N   UNK     0      14.067   3.776   0.000  0.00  0.00           N+0
HETATM   21  C   UNK     0      11.394   0.692   0.000  0.00  0.00           C+0
HETATM   22  N   UNK     0      12.729   1.463   0.000  0.00  0.00           N+0
HETATM   23  C   UNK     0      12.729   3.005   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      11.394   3.776   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      10.059   3.005   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0      10.059   1.463   0.000  0.00  0.00           N+0
HETATM   27  O   UNK     0       7.473   1.619   0.000  0.00  0.00           O+0
HETATM   28  C   UNK     0       8.720   0.712   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0       8.244  -0.754   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       6.702  -0.754   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0       6.225   0.712   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      -8.423   1.436   0.000  0.00  0.00           C+0
HETATM   33  O   UNK     0      -8.423   2.876   0.000  0.00  0.00           O+0
HETATM   34  C   UNK     0      -9.756   0.665   0.000  0.00  0.00           C+0
HETATM   35  C   UNK     0     -11.089   1.436   0.000  0.00  0.00           C+0
HETATM   36  C   UNK     0     -12.422   0.665   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0     -13.962   0.665   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0     -15.295   1.436   0.000  0.00  0.00           C+0
HETATM   39  C   UNK     0     -16.628   0.665   0.000  0.00  0.00           C+0
HETATM   40  C   UNK     0     -18.168   0.665   0.000  0.00  0.00           C+0
HETATM   41  C   UNK     0     -19.501   1.436   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -20.834   0.665   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -22.374   0.665   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -23.707   1.436   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -25.040   0.665   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -26.580   0.665   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -27.913   1.436   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -29.246   0.665   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -30.786   0.665   0.000  0.00  0.00           C+0
HETATM   50  C   UNK     0     -32.119   1.436   0.000  0.00  0.00           C+0
HETATM   51  C   UNK     0     -33.452   0.665   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -34.785   1.436   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -36.118   0.665   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -37.451   1.436   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      -6.551  -1.383   0.000  0.00  0.00           C+0
HETATM   56  O   UNK     0      -6.551  -2.823   0.000  0.00  0.00           O+0
HETATM   57  C   UNK     0      -7.884  -0.612   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      -9.217  -1.383   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0     -10.550  -0.612   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0     -12.090  -0.612   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0     -13.423  -1.383   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0     -14.756  -0.612   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -16.296  -0.612   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -17.629  -1.383   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -18.962  -0.612   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0     -20.502  -0.612   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0     -21.835  -1.383   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0     -23.168  -0.612   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0     -24.708  -0.612   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0     -26.041  -1.383   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0     -27.374  -0.612   0.000  0.00  0.00           C+0
HETATM   72  O   UNK     0     -27.374   0.828   0.000  0.00  0.00           O+0
HETATM   73  C   UNK     0     -28.707  -1.383   0.000  0.00  0.00           C+0
HETATM   74  C   UNK     0     -30.040  -0.612   0.000  0.00  0.00           C+0
HETATM   75  C   UNK     0     -31.373  -1.383   0.000  0.00  0.00           C+0
HETATM   76  C   UNK     0     -32.913  -1.383   0.000  0.00  0.00           C+0
HETATM   77  C   UNK     0     -34.246  -0.612   0.000  0.00  0.00           C+0
HETATM   78  C   UNK     0     -35.579  -1.383   0.000  0.00  0.00           C+0
CONECT    1   32    2                                                       
CONECT    2    1    3                                                       
CONECT    3    2    5    6    4                                             
CONECT    4    3   14                                                       
CONECT    5    3                                                            
CONECT    6    3   55                                                       
CONECT    7   29                                                            
CONECT    8   30                                                            
CONECT    9   10   31                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   17   18                                             
CONECT   12   11   13                                                       
CONECT   13   12   14   15   16                                             
CONECT   14   13    4                                                       
CONECT   15   13                                                            
CONECT   16   13                                                            
CONECT   17   11                                                            
CONECT   18   11                                                            
CONECT   19   21                                                            
CONECT   20   23                                                            
CONECT   21   22   19   26                                                  
CONECT   22   21   23                                                       
CONECT   23   22   24   20                                                  
CONECT   24   23   25                                                       
CONECT   25   24   26                                                       
CONECT   26   25   21   28                                                  
CONECT   27   28   31                                                       
CONECT   28   27   29   26                                                  
CONECT   29   28   30    7                                                  
CONECT   30   29   31    8                                                  
CONECT   31   27   30    9                                                  
CONECT   32    1   33   34                                                  
CONECT   33   32                                                            
CONECT   34   32   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37                                                       
CONECT   37   36   38                                                       
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   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                                                            
CONECT   55    6   56   57                                                  
CONECT   56   55                                                            
CONECT   57   55   58                                                       
CONECT   58   57   59                                                       
CONECT   59   58   60                                                       
CONECT   60   59   61                                                       
CONECT   61   60   62                                                       
CONECT   62   61   63                                                       
CONECT   63   62   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64   66                                                       
CONECT   66   65   67                                                       
CONECT   67   66   68                                                       
CONECT   68   67   69                                                       
CONECT   69   68   70                                                       
CONECT   70   69   71                                                       
CONECT   71   70   72   73                                                  
CONECT   72   71   73                                                       
CONECT   73   71   72   74                                                  
CONECT   74   73   75                                                       
CONECT   75   74   76                                                       
CONECT   76   75   77                                                       
CONECT   77   76   78                                                       
CONECT   78   77                                                            
MASTER        0    0    0    0    0    0    0    0   78    0  160    0
END
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3D PDB for HMDB0292513 (CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)))

COMPND    HMDB0292513
HETATM    1  C1  UNL     1      -3.880  -4.953  -1.431  1.00  0.00           C  
HETATM    2  C2  UNL     1      -4.514  -5.378  -2.751  1.00  0.00           C  
HETATM    3  C3  UNL     1      -3.559  -5.243  -3.866  1.00  0.00           C  
HETATM    4  C4  UNL     1      -3.795  -4.470  -4.887  1.00  0.00           C  
HETATM    5  C5  UNL     1      -4.960  -3.629  -5.146  1.00  0.00           C  
HETATM    6  C6  UNL     1      -4.555  -2.143  -5.312  1.00  0.00           C  
HETATM    7  O1  UNL     1      -3.596  -2.128  -6.452  1.00  0.00           O  
HETATM    8  C7  UNL     1      -4.868  -1.462  -6.525  1.00  0.00           C  
HETATM    9  C8  UNL     1      -4.835   0.013  -6.720  1.00  0.00           C  
HETATM   10  C9  UNL     1      -5.743   0.714  -5.823  1.00  0.00           C  
HETATM   11  C10 UNL     1      -5.354   1.697  -5.042  1.00  0.00           C  
HETATM   12  C11 UNL     1      -4.020   2.266  -4.908  1.00  0.00           C  
HETATM   13  C12 UNL     1      -3.562   2.261  -3.505  1.00  0.00           C  
HETATM   14  C13 UNL     1      -2.509   1.651  -3.080  1.00  0.00           C  
HETATM   15  C14 UNL     1      -1.577   0.828  -3.966  1.00  0.00           C  
HETATM   16  C15 UNL     1      -1.543  -0.515  -3.305  1.00  0.00           C  
HETATM   17  C16 UNL     1      -0.415  -1.010  -2.937  1.00  0.00           C  
HETATM   18  C17 UNL     1       0.948  -0.401  -3.102  1.00  0.00           C  
HETATM   19  C18 UNL     1       1.701  -1.512  -3.760  1.00  0.00           C  
HETATM   20  C19 UNL     1       2.785  -1.936  -3.209  1.00  0.00           C  
HETATM   21  C20 UNL     1       3.415  -1.475  -2.006  1.00  0.00           C  
HETATM   22  C21 UNL     1       3.570  -2.475  -0.933  1.00  0.00           C  
HETATM   23  C22 UNL     1       2.313  -2.886  -0.290  1.00  0.00           C  
HETATM   24  O2  UNL     1       2.092  -4.144  -0.108  1.00  0.00           O  
HETATM   25  O3  UNL     1       1.326  -2.079   0.170  1.00  0.00           O  
HETATM   26  C23 UNL     1       0.160  -2.322   0.852  1.00  0.00           C  
HETATM   27  C24 UNL     1      -1.146  -2.024   0.202  1.00  0.00           C  
HETATM   28  O4  UNL     1      -2.154  -2.247   1.213  1.00  0.00           O  
HETATM   29  C25 UNL     1      -3.490  -2.019   0.926  1.00  0.00           C  
HETATM   30  O5  UNL     1      -3.777  -1.637  -0.234  1.00  0.00           O  
HETATM   31  C26 UNL     1      -4.577  -2.205   1.944  1.00  0.00           C  
HETATM   32  C27 UNL     1      -4.860  -0.806   2.568  1.00  0.00           C  
HETATM   33  C28 UNL     1      -3.625  -0.312   3.183  1.00  0.00           C  
HETATM   34  C29 UNL     1      -2.996   0.752   2.810  1.00  0.00           C  
HETATM   35  C30 UNL     1      -3.395   1.653   1.711  1.00  0.00           C  
HETATM   36  C31 UNL     1      -3.539   3.044   2.168  1.00  0.00           C  
HETATM   37  C32 UNL     1      -2.764   4.017   1.653  1.00  0.00           C  
HETATM   38  C33 UNL     1      -1.746   3.690   0.611  1.00  0.00           C  
HETATM   39  C34 UNL     1      -0.417   4.096   1.100  1.00  0.00           C  
HETATM   40  C35 UNL     1       0.384   4.928   0.486  1.00  0.00           C  
HETATM   41  C36 UNL     1      -0.020   5.542  -0.804  1.00  0.00           C  
HETATM   42  C37 UNL     1       0.912   5.098  -1.854  1.00  0.00           C  
HETATM   43  C38 UNL     1       1.640   5.862  -2.600  1.00  0.00           C  
HETATM   44  C39 UNL     1       1.642   7.324  -2.509  1.00  0.00           C  
HETATM   45  C40 UNL     1       3.017   7.839  -2.221  1.00  0.00           C  
HETATM   46  C41 UNL     1       3.593   8.638  -3.079  1.00  0.00           C  
HETATM   47  C42 UNL     1       3.015   9.109  -4.351  1.00  0.00           C  
HETATM   48  C43 UNL     1       3.891   8.676  -5.539  1.00  0.00           C  
HETATM   49  C44 UNL     1       5.283   9.215  -5.442  1.00  0.00           C  
HETATM   50  C45 UNL     1       5.336  10.726  -5.416  1.00  0.00           C  
HETATM   51  C46 UNL     1       6.777  11.216  -5.324  1.00  0.00           C  
HETATM   52  C47 UNL     1       0.271  -1.581   2.190  1.00  0.00           C  
HETATM   53  O6  UNL     1       1.363  -2.036   2.904  1.00  0.00           O  
HETATM   54  P1  UNL     1       1.541  -1.204   4.367  1.00  0.00           P  
HETATM   55  O7  UNL     1       0.933   0.177   4.211  1.00  0.00           O  
HETATM   56  O8  UNL     1       0.777  -2.068   5.571  1.00  0.00           O  
HETATM   57  O9  UNL     1       3.191  -1.123   4.691  1.00  0.00           O  
HETATM   58  P2  UNL     1       3.570  -2.269   5.867  1.00  0.00           P  
HETATM   59  O10 UNL     1       4.902  -2.950   5.547  1.00  0.00           O  
HETATM   60  O11 UNL     1       3.589  -1.591   7.420  1.00  0.00           O  
HETATM   61  O12 UNL     1       2.382  -3.479   5.824  1.00  0.00           O  
HETATM   62  C48 UNL     1       2.378  -4.180   7.025  1.00  0.00           C  
HETATM   63  C49 UNL     1       1.335  -5.264   7.052  1.00  0.00           C  
HETATM   64  O13 UNL     1       1.460  -6.216   6.077  1.00  0.00           O  
HETATM   65  C50 UNL     1       1.952  -7.400   6.678  1.00  0.00           C  
HETATM   66  N1  UNL     1       3.346  -7.429   6.531  1.00  0.00           N  
HETATM   67  C51 UNL     1       3.865  -6.782   5.451  1.00  0.00           C  
HETATM   68  C52 UNL     1       5.214  -6.726   5.185  1.00  0.00           C  
HETATM   69  C53 UNL     1       6.118  -7.359   6.055  1.00  0.00           C  
HETATM   70  N2  UNL     1       7.511  -7.316   5.818  1.00  0.00           N  
HETATM   71  N3  UNL     1       5.560  -7.979   7.099  1.00  0.00           N  
HETATM   72  C54 UNL     1       4.239  -8.017   7.331  1.00  0.00           C  
HETATM   73  O14 UNL     1       3.837  -8.619   8.325  1.00  0.00           O  
HETATM   74  C55 UNL     1       1.301  -7.403   7.983  1.00  0.00           C  
HETATM   75  O15 UNL     1      -0.071  -7.707   7.769  1.00  0.00           O  
HETATM   76  C56 UNL     1       1.312  -5.951   8.402  1.00  0.00           C  
HETATM   77  O16 UNL     1       0.157  -5.567   9.079  1.00  0.00           O  
HETATM   78  H1  UNL     1      -2.882  -4.504  -1.677  1.00  0.00           H  
HETATM   79  H2  UNL     1      -3.716  -5.826  -0.790  1.00  0.00           H  
HETATM   80  H3  UNL     1      -4.476  -4.210  -0.903  1.00  0.00           H  
HETATM   81  H4  UNL     1      -5.493  -4.916  -2.900  1.00  0.00           H  
HETATM   82  H5  UNL     1      -4.737  -6.482  -2.641  1.00  0.00           H  
HETATM   83  H6  UNL     1      -2.613  -5.812  -3.837  1.00  0.00           H  
HETATM   84  H7  UNL     1      -3.006  -4.438  -5.676  1.00  0.00           H  
HETATM   85  H8  UNL     1      -5.380  -3.935  -6.146  1.00  0.00           H  
HETATM   86  H9  UNL     1      -5.762  -3.640  -4.416  1.00  0.00           H  
HETATM   87  H10 UNL     1      -4.208  -1.665  -4.419  1.00  0.00           H  
HETATM   88  H11 UNL     1      -5.495  -2.029  -7.283  1.00  0.00           H  
HETATM   89  H12 UNL     1      -5.180   0.263  -7.775  1.00  0.00           H  
HETATM   90  H13 UNL     1      -3.769   0.327  -6.614  1.00  0.00           H  
HETATM   91  H14 UNL     1      -6.795   0.375  -5.832  1.00  0.00           H  
HETATM   92  H15 UNL     1      -6.155   2.135  -4.414  1.00  0.00           H  
HETATM   93  H16 UNL     1      -3.238   1.877  -5.551  1.00  0.00           H  
HETATM   94  H17 UNL     1      -4.057   3.381  -5.204  1.00  0.00           H  
HETATM   95  H18 UNL     1      -4.146   2.820  -2.730  1.00  0.00           H  
HETATM   96  H19 UNL     1      -2.210   1.685  -2.030  1.00  0.00           H  
HETATM   97  H20 UNL     1      -0.614   1.311  -3.873  1.00  0.00           H  
HETATM   98  H21 UNL     1      -1.946   0.664  -4.964  1.00  0.00           H  
HETATM   99  H22 UNL     1      -2.451  -1.045  -3.121  1.00  0.00           H  
HETATM  100  H23 UNL     1      -0.409  -2.012  -2.468  1.00  0.00           H  
HETATM  101  H24 UNL     1       1.252  -0.117  -2.116  1.00  0.00           H  
HETATM  102  H25 UNL     1       0.927   0.479  -3.739  1.00  0.00           H  
HETATM  103  H26 UNL     1       1.312  -1.921  -4.666  1.00  0.00           H  
HETATM  104  H27 UNL     1       3.310  -2.783  -3.734  1.00  0.00           H  
HETATM  105  H28 UNL     1       4.480  -1.087  -2.271  1.00  0.00           H  
HETATM  106  H29 UNL     1       2.979  -0.565  -1.526  1.00  0.00           H  
HETATM  107  H30 UNL     1       4.119  -3.409  -1.316  1.00  0.00           H  
HETATM  108  H31 UNL     1       4.257  -2.101  -0.112  1.00  0.00           H  
HETATM  109  H32 UNL     1       0.115  -3.425   1.109  1.00  0.00           H  
HETATM  110  H33 UNL     1      -1.333  -2.850  -0.527  1.00  0.00           H  
HETATM  111  H34 UNL     1      -1.299  -1.022  -0.174  1.00  0.00           H  
HETATM  112  H35 UNL     1      -4.338  -2.899   2.735  1.00  0.00           H  
HETATM  113  H36 UNL     1      -5.492  -2.482   1.420  1.00  0.00           H  
HETATM  114  H37 UNL     1      -5.412  -0.197   1.895  1.00  0.00           H  
HETATM  115  H38 UNL     1      -5.555  -1.075   3.427  1.00  0.00           H  
HETATM  116  H39 UNL     1      -3.230  -0.910   4.026  1.00  0.00           H  
HETATM  117  H40 UNL     1      -2.065   1.020   3.364  1.00  0.00           H  
HETATM  118  H41 UNL     1      -2.909   1.467   0.769  1.00  0.00           H  
HETATM  119  H42 UNL     1      -4.497   1.345   1.495  1.00  0.00           H  
HETATM  120  H43 UNL     1      -4.250   3.357   2.918  1.00  0.00           H  
HETATM  121  H44 UNL     1      -2.860   5.042   1.979  1.00  0.00           H  
HETATM  122  H45 UNL     1      -2.060   4.179  -0.298  1.00  0.00           H  
HETATM  123  H46 UNL     1      -1.683   2.600   0.378  1.00  0.00           H  
HETATM  124  H47 UNL     1      -0.071   3.679   2.043  1.00  0.00           H  
HETATM  125  H48 UNL     1       1.340   5.178   0.911  1.00  0.00           H  
HETATM  126  H49 UNL     1      -1.062   5.382  -1.050  1.00  0.00           H  
HETATM  127  H50 UNL     1       0.080   6.649  -0.652  1.00  0.00           H  
HETATM  128  H51 UNL     1       1.000   4.012  -2.025  1.00  0.00           H  
HETATM  129  H52 UNL     1       2.297   5.396  -3.358  1.00  0.00           H  
HETATM  130  H53 UNL     1       1.033   7.663  -1.653  1.00  0.00           H  
HETATM  131  H54 UNL     1       1.202   7.783  -3.405  1.00  0.00           H  
HETATM  132  H55 UNL     1       3.538   7.550  -1.311  1.00  0.00           H  
HETATM  133  H56 UNL     1       4.618   9.018  -2.851  1.00  0.00           H  
HETATM  134  H57 UNL     1       2.007   8.832  -4.576  1.00  0.00           H  
HETATM  135  H58 UNL     1       3.054  10.239  -4.293  1.00  0.00           H  
HETATM  136  H59 UNL     1       3.402   8.936  -6.478  1.00  0.00           H  
HETATM  137  H60 UNL     1       3.960   7.561  -5.475  1.00  0.00           H  
HETATM  138  H61 UNL     1       5.802   8.847  -4.532  1.00  0.00           H  
HETATM  139  H62 UNL     1       5.870   8.897  -6.331  1.00  0.00           H  
HETATM  140  H63 UNL     1       4.843  11.190  -6.294  1.00  0.00           H  
HETATM  141  H64 UNL     1       4.820  11.145  -4.509  1.00  0.00           H  
HETATM  142  H65 UNL     1       6.995  11.921  -6.149  1.00  0.00           H  
HETATM  143  H66 UNL     1       7.489  10.365  -5.419  1.00  0.00           H  
HETATM  144  H67 UNL     1       6.989  11.745  -4.392  1.00  0.00           H  
HETATM  145  H68 UNL     1       0.313  -0.493   1.985  1.00  0.00           H  
HETATM  146  H69 UNL     1      -0.633  -1.769   2.802  1.00  0.00           H  
HETATM  147  H70 UNL     1      -0.036  -1.602   5.886  1.00  0.00           H  
HETATM  148  H71 UNL     1       4.172  -0.812   7.453  1.00  0.00           H  
HETATM  149  H72 UNL     1       3.400  -4.542   7.198  1.00  0.00           H  
HETATM  150  H73 UNL     1       2.081  -3.452   7.842  1.00  0.00           H  
HETATM  151  H74 UNL     1       0.349  -4.741   6.882  1.00  0.00           H  
HETATM  152  H75 UNL     1       1.518  -8.222   6.037  1.00  0.00           H  
HETATM  153  H76 UNL     1       3.198  -6.274   4.737  1.00  0.00           H  
HETATM  154  H77 UNL     1       5.624  -6.208   4.326  1.00  0.00           H  
HETATM  155  H78 UNL     1       7.902  -7.430   4.869  1.00  0.00           H  
HETATM  156  H79 UNL     1       8.157  -7.163   6.611  1.00  0.00           H  
HETATM  157  H80 UNL     1       1.623  -8.103   8.744  1.00  0.00           H  
HETATM  158  H81 UNL     1      -0.425  -7.173   7.012  1.00  0.00           H  
HETATM  159  H82 UNL     1       2.161  -5.676   9.033  1.00  0.00           H  
HETATM  160  H83 UNL     1      -0.140  -4.648   8.882  1.00  0.00           H  
CONECT    1    2   78   79   80
CONECT    2    3   81   82
CONECT    3    4    4   83
CONECT    4    5   84
CONECT    5    6   85   86
CONECT    6    7    8   87
CONECT    7    8
CONECT    8    9   88
CONECT    9   10   89   90
CONECT   10   11   11   91
CONECT   11   12   92
CONECT   12   13   93   94
CONECT   13   14   14   95
CONECT   14   15   96
CONECT   15   16   97   98
CONECT   16   17   17   99
CONECT   17   18  100
CONECT   18   19  101  102
CONECT   19   20   20  103
CONECT   20   21  104
CONECT   21   22  105  106
CONECT   22   23  107  108
CONECT   23   24   24   25
CONECT   25   26
CONECT   26   27   52  109
CONECT   27   28  110  111
CONECT   28   29
CONECT   29   30   30   31
CONECT   31   32  112  113
CONECT   32   33  114  115
CONECT   33   34   34  116
CONECT   34   35  117
CONECT   35   36  118  119
CONECT   36   37   37  120
CONECT   37   38  121
CONECT   38   39  122  123
CONECT   39   40   40  124
CONECT   40   41  125
CONECT   41   42  126  127
CONECT   42   43   43  128
CONECT   43   44  129
CONECT   44   45  130  131
CONECT   45   46   46  132
CONECT   46   47  133
CONECT   47   48  134  135
CONECT   48   49  136  137
CONECT   49   50  138  139
CONECT   50   51  140  141
CONECT   51  142  143  144
CONECT   52   53  145  146
CONECT   53   54
CONECT   54   55   55   56   57
CONECT   56  147
CONECT   57   58
CONECT   58   59   59   60   61
CONECT   60  148
CONECT   61   62
CONECT   62   63  149  150
CONECT   63   64   76  151
CONECT   64   65
CONECT   65   66   74  152
CONECT   66   67   72
CONECT   67   68   68  153
CONECT   68   69  154
CONECT   69   70   71   71
CONECT   70  155  156
CONECT   71   72
CONECT   72   73   73
CONECT   74   75   76  157
CONECT   75  158
CONECT   76   77  159
CONECT   77  160
END
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SMILES for HMDB0292513 (CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)))

[H][C@@](COC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)OC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/CC1OC1C\C=C/CC
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INCHI for HMDB0292513 (CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)))

InChI=1S/C56H83N3O16P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-22-25-28-31-35-39-51(60)69-43-46(72-52(61)40-36-32-29-26-23-20-19-21-24-27-30-34-38-48-47(73-48)37-33-6-4-2)44-70-76(65,66)75-77(67,68)71-45-49-53(62)54(63)55(74-49)59-42-41-50(57)58-56(59)64/h6,9-10,12-13,15-16,18,20-24,28-34,41-42,46-49,53-55,62-63H,3-5,7-8,11,14,17,19,25-27,35-40,43-45H2,1-2H3,(H,65,66)(H,67,68)(H2,57,58,64)/b10-9-,13-12-,16-15-,22-18-,23-20-,24-21-,31-28-,32-29-,33-6-,34-30-/t46-,47?,48?,49-,53-,54-,55-/m1/s1
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Synonyms
ValueSource
{[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({[(2R)-3-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-2-{[(4Z,7Z,10Z,13Z)-15-{3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}pentadeca-4,7,10,13-tetraenoyl]oxy}propoxy](hydroxy)phosphoryl}oxy)phosphinateGenerator
Chemical FormulaC56H83N3O16P2
Average Molecular Weight1116.233
Monoisotopic Molecular Weight1115.524857601
IUPAC Name{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2R)-3-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-2-{[(4Z,7Z,10Z,13Z)-15-{3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}pentadeca-4,7,10,13-tetraenoyl]oxy}propoxy](hydroxy)phosphoryl}oxy)phosphinic acid
Traditional Name[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([(2R)-3-[(4Z,7Z,10Z,13Z,16Z)-docosa-4,7,10,13,16-pentaenoyloxy]-2-{[(4Z,7Z,10Z,13Z)-15-{3-[(2Z)-pent-2-en-1-yl]oxiran-2-yl}pentadeca-4,7,10,13-tetraenoyl]oxy}propoxy(hydroxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/C\C=C/CCCCC)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1O)N1C=CC(N)=NC1=O)OC(=O)CC\C=C/C\C=C/C\C=C/C\C=C/CC1OC1C\C=C/CC
InChI Identifier
InChI=1S/C56H83N3O16P2/c1-3-5-7-8-9-10-11-12-13-14-15-16-17-18-22-25-28-31-35-39-51(60)69-43-46(72-52(61)40-36-32-29-26-23-20-19-21-24-27-30-34-38-48-47(73-48)37-33-6-4-2)44-70-76(65,66)75-77(67,68)71-45-49-53(62)54(63)55(74-49)59-42-41-50(57)58-56(59)64/h6,9-10,12-13,15-16,18,20-24,28-34,41-42,46-49,53-55,62-63H,3-5,7-8,11,14,17,19,25-27,35-40,43-45H2,1-2H3,(H,65,66)(H,67,68)(H2,57,58,64)/b10-9-,13-12-,16-15-,22-18-,23-20-,24-21-,31-28-,32-29-,33-6-,34-30-/t46-,47?,48?,49-,53-,54-,55-/m1/s1
InChI KeyDMZKNSXMKRALSL-OKRMPEIJSA-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
logP7.01ALOGPS
logP9.97ChemAxon
logS-5.9ALOGPS
pKa (Strongest Acidic)1.86ChemAxon
pKa (Strongest Basic)-0.032ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count13ChemAxon
Hydrogen Donor Count5ChemAxon
Polar Surface Area275.8 ŲChemAxon
Rotatable Bond Count43ChemAxon
Refractivity306.11 m³·mol⁻¹ChemAxon
Polarizability116.58 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+325.14532859911
AllCCS[M+H-H2O]+325.62332859911
AllCCS[M+Na]+324.52832859911
AllCCS[M+NH4]+324.67132859911
AllCCS[M-H]-311.99532859911
AllCCS[M+Na-2H]-318.13732859911
AllCCS[M+HCOO]-324.75232859911
DeepCCS[M+H]+284.72530932474
DeepCCS[M-H]-283.07230932474
DeepCCS[M-2H]-317.10530932474
DeepCCS[M+Na]+290.88230932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)) 10V, Negative-QTOFsplash10-03di-1901000400-58af376aeea4030206462021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)) 20V, Negative-QTOFsplash10-002f-9207710430-ae2be6dbcedc3a28be012021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)) 40V, Negative-QTOFsplash10-0a4i-8329200210-e33dbc38ba6b98f4c3bf2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)) 10V, Positive-QTOFsplash10-014j-9500000101-b718143e30a2994e9e882021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)) 20V, Positive-QTOFsplash10-001j-9000000001-7934783a2517586d7bd42021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(22:5(4Z,7Z,10Z,13Z,16Z)/22:5(4Z,7Z,10Z,13Z,19Z)-O(16,17)) 40V, Positive-QTOFsplash10-00di-2019300000-cfc75d10877748cdff5a2021-10-21Wishart 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 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 ]