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Showing metabocard for CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0) (HMDB0290805)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-16 19:03:51 UTC
Update Date2022-11-30 20:07:19 UTC
HMDB IDHMDB0290805
Secondary Accession NumbersNone
Metabolite Identification
Common NameCDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0)
DescriptionCDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0) 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(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0), in particular, consists of one chain of one Lipoxin A4 at the C-1 position and one chain of hexadecanoyl 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 HMDB0290805 (CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0))

CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0)
  Mrv1652309162121042D          

 72 73  0  0  1  0            999 V2000
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M  END
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3D MOL for HMDB0290805 (CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0))

HMDB0290805
     RDKit          3D
CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0)
152153  0  0  0  0  0  0  0  0999 V2000
    1.2143    2.8728   -7.6145 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3048    2.8667   -6.1120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0091    2.5121   -5.4475 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2235    2.5452   -3.9486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0930    2.2073   -3.2667 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9686    2.2183   -1.7727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0048    1.2301   -1.2086 C   0  0  0  0  0  0  0  0  0  0  0  0
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    4.3109    2.1717    0.1657 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3033    1.1803    0.6684 C   0  0  0  0  0  0  0  0  0  0  0  0
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    3.4609   -2.9249   -0.2240 O   0  0  0  0  0  0  0  0  0  0  0  0
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    2.5010    2.7309    6.3956 C   0  0  1  0  0  0  0  0  0  0  0  0
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    2.9875    4.4110    5.1631 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7586    5.0773    4.1801 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1021    4.8328    4.2075 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9748    5.3964    3.3323 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4985    6.2566    2.3664 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3778    6.8641    1.4381 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1776    6.4817    2.3577 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3226    5.9135    3.2352 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0863    6.1538    3.1911 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5262    4.3699    5.0258 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8785    5.5425    5.4199 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1440    3.2695    6.0207 C   0  0  2  0  0  0  0  0  0  0  0  0
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M  END
Download

3D SDF for HMDB0290805 (CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0))

CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0)
  Mrv1652309162121042D          

 72 73  0  0  1  0            999 V2000
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 70 71  1  0  0  0  0
 71 72  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0290805

> <DATABASE_NAME>
hmdb

> <SMILES>
[H][C@@](COC(=O)CCC[C@@H](O)[C@H](O)\C=C\C=C\C=C/C=C/[C@H](O)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)CCCCCCCCCCCCCCC

> <INCHI_IDENTIFIER>
InChI=1S/C48H81N3O18P2/c1-3-5-7-8-9-10-11-12-13-14-15-20-24-30-44(56)67-38(34-64-43(55)31-25-29-40(54)39(53)28-23-19-17-16-18-22-27-37(52)26-21-6-4-2)35-65-70(60,61)69-71(62,63)66-36-41-45(57)46(58)47(68-41)51-33-32-42(49)50-48(51)59/h16-19,22-23,27-28,32-33,37-41,45-47,52-54,57-58H,3-15,20-21,24-26,29-31,34-36H2,1-2H3,(H,60,61)(H,62,63)(H2,49,50,59)/b18-16-,19-17+,27-22+,28-23+/t37-,38-,39-,40-,41-,45-,46-,47-/m1/s1

> <INCHI_KEY>
ZYNASFISMGAGIS-VEDJJGNASA-N

> <FORMULA>
C48H81N3O18P2

> <MOLECULAR_WEIGHT>
1050.127

> <EXACT_MASS>
1049.499036776

> <JCHEM_ACCEPTOR_COUNT>
15

> <JCHEM_ATOM_COUNT>
152

> <JCHEM_AVERAGE_POLARIZABILITY>
112.00625176242542

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
8

> <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)-2-(hexadecanoyloxy)-3-{[(5R,6R,7E,9E,11Z,13E,15R)-5,6,15-trihydroxyicosa-7,9,11,13-tetraenoyl]oxy}propoxy](hydroxy)phosphoryl}oxy)phosphinic acid

> <ALOGPS_LOGP>
4.76

> <JCHEM_LOGP>
6.350812071000002

> <ALOGPS_LOGS>
-4.99

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
2

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
1.863318882085685

> <JCHEM_PKA_STRONGEST_ACIDIC>
-0.019931893349512286

> <JCHEM_PKA_STRONGEST_BASIC>
3.2716317100108894

> <JCHEM_POLAR_SURFACE_AREA>
323.96000000000004

> <JCHEM_REFRACTIVITY>
267.4734

> <JCHEM_ROTATABLE_BOND_COUNT>
42

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.09e-02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-5-(4-amino-2-oxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy([(2R)-2-(hexadecanoyloxy)-3-{[(5R,6R,7E,9E,11Z,13E,15R)-5,6,15-trihydroxyicosa-7,9,11,13-tetraenoyl]oxy}propoxy(hydroxy)phosphoryl]oxy)phosphinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0290805 (CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0))

HMDB0290805
     RDKit          3D
CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0)
152153  0  0  0  0  0  0  0  0999 V2000
    1.2143    2.8728   -7.6145 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.3048    2.8667   -6.1120 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0091    2.5121   -5.4475 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.2235    2.5452   -3.9486 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0930    2.2073   -3.2667 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9686    2.2183   -1.7727 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0048    1.2301   -1.2086 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0794    1.3097    0.3038 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5693    2.6709    0.7537 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.9516    2.9645    0.2029 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.9361    1.9200    0.7298 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.3109    2.1717    0.1657 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3033    1.1803    0.6684 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4927    1.2148    2.1474 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.4822    0.2434    2.6939 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1778   -1.1691    2.4859 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0392   -2.0196    2.9005 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.0347   -1.6394    1.8821 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8535   -3.0427    1.7523 C   0  0  2  0  0  0  0  0  0  0  0  0
    4.6408   -3.4901    0.3444 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.4609   -2.9249   -0.2240 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1099   -3.2511   -1.5213 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8642   -4.0364   -2.1486 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9009   -2.7335   -2.2120 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8070   -3.2721   -3.6216 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5481   -2.7410   -4.3079 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4574   -3.2513   -5.7174 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.4092   -4.6289   -5.8206 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5679   -2.5604   -6.5687 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.5348   -1.1879   -6.4044 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8780   -3.1880   -6.4296 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8029   -2.9102   -5.5282 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0598   -3.6108   -5.5057 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0463   -3.4022   -4.6396 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.2405   -4.2014   -4.7691 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2555   -4.0723   -3.9716 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2709   -3.1113   -2.8839 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.3307   -3.0058   -2.0812 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5461   -2.1303   -0.9613 C   0  0  2  0  0  0  0  0  0  0  0  0
   -9.8967   -1.7201   -0.8860 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6282   -0.9039   -0.8969 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.9811   -0.0903    0.3098 C   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2744    1.1682    0.5404 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.8026    1.1755    0.7301 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.0583    0.7358   -0.4942 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.6452   -3.4487    2.6176 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.8672   -3.1151    3.9439 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5693   -3.5214    4.9293 P   0  0  0  0  0  5  0  0  0  0  0  0
    2.9899   -4.0174    6.2907 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6863   -4.7470    4.1329 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5965   -2.1496    5.1098 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1946   -1.1190    6.3039 P   0  0  0  0  0  5  0  0  0  0  0  0
    1.3152   -1.2919    7.5268 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.7877   -1.5063    6.6769 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0911    0.4878    5.7282 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5305    1.2885    6.7533 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.5010    2.7309    6.3956 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.3229    3.0419    5.2821 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.9875    4.4110    5.1631 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7586    5.0773    4.1801 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1021    4.8328    4.2075 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9748    5.3964    3.3323 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4985    6.2566    2.3664 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3778    6.8641    1.4381 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.1776    6.4817    2.3577 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.3226    5.9135    3.2352 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.0863    6.1538    3.1911 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.5262    4.3699    5.0258 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8785    5.5425    5.4199 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1440    3.2695    6.0207 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5110    3.8412    7.1469 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2526    3.2859   -7.9779 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0883    3.4509   -7.9888 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.3493    1.8256   -7.9705 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6995    3.8319   -5.7699 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0400    2.0640   -5.8336 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7777    3.2392   -5.7467 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3359    1.5277   -5.7987 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5440    3.5485   -3.6267 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9701    1.8059   -3.6448 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4307    1.1964   -3.6379 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8328    2.9127   -3.6521 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0020    2.0259   -1.3687 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7380    3.2562   -1.4451 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9963    1.3494   -1.6771 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3714    0.2062   -1.4417 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7016    0.4810    0.6576 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9413    1.1830    0.6841 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.6682    2.6234    1.8652 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1695    3.4407    0.5246 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9731    2.9715   -0.8968 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2786    3.9432    0.5548 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.6177    0.9086    0.3587 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9181    1.9022    1.8383 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.2203    2.1330   -0.9405 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6451    3.2057    0.4413 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.0123    0.1621    0.2993 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2998    1.3941    0.2068 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.8590    2.2425    2.4368 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.5364    1.1077    2.7156 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.4998    0.5220    2.2823 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5772    0.4548    3.7850 H   0  0  0  0  0  0  0  0  0  0  0  0
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    4.5407   -4.6025    0.3603 H   0  0  0  0  0  0  0  0  0  0  0  0
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    1.9089   -1.6248   -2.2814 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -4.2110   -4.3900   -6.2789 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.9067   -2.6564   -3.8924 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.3062   -4.9649   -5.5840 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1232   -4.7345   -4.1549 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4628   -2.4397   -2.6550 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1443   -3.7110   -2.3485 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -5.6856    0.7483   -1.4019 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.2351    1.5018   -0.6748 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.7346   -2.9429    2.1927 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4857   -4.5392    2.5195 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7730   -4.4676    3.9234 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1001   -0.9836    7.4562 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.9787    1.1656    7.7013 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.5986    1.0185    6.9308 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.9063    3.3701    7.2302 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2415    4.8361    6.1550 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5335    4.1520    4.9582 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.0388    5.1853    3.3746 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.1724    7.4427    1.7551 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2406    6.7395    0.4162 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.1552    4.0044    4.0448 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4564    6.1398    5.9490 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4776    2.5146    5.5713 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3500    4.2358    6.8023 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  3  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  1  0
  7  8  1  0
  8  9  1  0
  9 10  1  0
 10 11  1  0
 11 12  1  0
 12 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  2  0
 16 18  1  0
 18 19  1  0
 19 20  1  0
 20 21  1  0
 21 22  1  0
 22 23  2  0
 22 24  1  0
 24 25  1  0
 25 26  1  0
 26 27  1  0
 27 28  1  0
 27 29  1  0
 29 30  1  0
 29 31  1  0
 31 32  2  0
 32 33  1  0
 33 34  2  0
 34 35  1  0
 35 36  2  0
 36 37  1  0
 37 38  2  0
 38 39  1  0
 39 40  1  0
 39 41  1  0
 41 42  1  0
 42 43  1  0
 43 44  1  0
 44 45  1  0
 19 46  1  0
 46 47  1  0
 47 48  1  0
 48 49  2  0
 48 50  1  0
 48 51  1  0
 51 52  1  0
 52 53  2  0
 52 54  1  0
 52 55  1  0
 55 56  1  0
 56 57  1  0
 57 58  1  0
 58 59  1  0
 59 60  1  0
 60 61  1  0
 61 62  2  0
 62 63  1  0
 63 64  1  0
 63 65  2  0
 65 66  1  0
 66 67  2  0
 59 68  1  0
 68 69  1  0
 68 70  1  0
 70 71  1  0
 70 57  1  0
 66 60  1  0
  1 72  1  0
  1 73  1  0
  1 74  1  0
  2 75  1  0
  2 76  1  0
  3 77  1  0
  3 78  1  0
  4 79  1  0
  4 80  1  0
  5 81  1  0
  5 82  1  0
  6 83  1  0
  6 84  1  0
  7 85  1  0
  7 86  1  0
  8 87  1  0
  8 88  1  0
  9 89  1  0
  9 90  1  0
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 11 94  1  0
 12 95  1  0
 12 96  1  0
 13 97  1  0
 13 98  1  0
 14 99  1  0
 14100  1  0
 15101  1  0
 15102  1  0
 19103  1  1
 20104  1  0
 20105  1  0
 24106  1  0
 24107  1  0
 25108  1  0
 25109  1  0
 26110  1  0
 26111  1  0
 27112  1  6
 28113  1  0
 29114  1  6
 30115  1  0
 31116  1  0
 32117  1  0
 33118  1  0
 34119  1  0
 35120  1  0
 36121  1  0
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 40125  1  0
 41126  1  0
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 50139  1  0
 54140  1  0
 56141  1  0
 56142  1  0
 57143  1  1
 59144  1  1
 61145  1  0
 62146  1  0
 64147  1  0
 64148  1  0
 68149  1  6
 69150  1  0
 70151  1  6
 71152  1  0
M  END
Download

PDB for HMDB0290805 (CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0))

HEADER    PROTEIN                                 16-SEP-21   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0)   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-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     -13.755   1.436   0.000  0.00  0.00           C+0
HETATM   38  O   UNK     0     -13.755   2.876   0.000  0.00  0.00           O+0
HETATM   39  C   UNK     0     -15.088   0.665   0.000  0.00  0.00           C+0
HETATM   40  O   UNK     0     -15.088  -0.775   0.000  0.00  0.00           O+0
HETATM   41  C   UNK     0     -16.421   1.436   0.000  0.00  0.00           C+0
HETATM   42  C   UNK     0     -17.754   0.665   0.000  0.00  0.00           C+0
HETATM   43  C   UNK     0     -19.087   1.436   0.000  0.00  0.00           C+0
HETATM   44  C   UNK     0     -20.420   0.665   0.000  0.00  0.00           C+0
HETATM   45  C   UNK     0     -21.753   1.436   0.000  0.00  0.00           C+0
HETATM   46  C   UNK     0     -23.293   1.436   0.000  0.00  0.00           C+0
HETATM   47  C   UNK     0     -24.626   0.665   0.000  0.00  0.00           C+0
HETATM   48  C   UNK     0     -25.959   1.436   0.000  0.00  0.00           C+0
HETATM   49  C   UNK     0     -27.292   0.665   0.000  0.00  0.00           C+0
HETATM   50  O   UNK     0     -27.292  -0.775   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0     -28.625   1.436   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0     -29.958   0.665   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0     -31.291   1.436   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0     -32.624   0.665   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0     -33.957   1.436   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      -6.551  -1.383   0.000  0.00  0.00           C+0
HETATM   57  O   UNK     0      -6.551  -2.823   0.000  0.00  0.00           O+0
HETATM   58  C   UNK     0      -7.884  -0.612   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      -9.217  -1.383   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0     -10.550  -0.612   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0     -11.883  -1.383   0.000  0.00  0.00           C+0
HETATM   62  C   UNK     0     -13.216  -0.612   0.000  0.00  0.00           C+0
HETATM   63  C   UNK     0     -14.549  -1.383   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0     -15.882  -0.612   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0     -17.215  -1.383   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0     -18.548  -0.612   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0     -19.881  -1.383   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0     -21.214  -0.612   0.000  0.00  0.00           C+0
HETATM   69  C   UNK     0     -22.547  -1.383   0.000  0.00  0.00           C+0
HETATM   70  C   UNK     0     -23.880  -0.612   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0     -25.213  -1.383   0.000  0.00  0.00           C+0
HETATM   72  C   UNK     0     -26.546  -0.612   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   56                                                       
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   39                                                  
CONECT   38   37                                                            
CONECT   39   37   40   41                                                  
CONECT   40   39                                                            
CONECT   41   39   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   51                                                  
CONECT   50   49                                                            
CONECT   51   49   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54                                                            
CONECT   56    6   57   58                                                  
CONECT   57   56                                                            
CONECT   58   56   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                                                       
CONECT   72   71                                                            
MASTER        0    0    0    0    0    0    0    0   72    0  146    0
END
Download

3D PDB for HMDB0290805 (CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0))

COMPND    HMDB0290805
HETATM    1  C1  UNL     1       1.214   2.873  -7.615  1.00  0.00           C  
HETATM    2  C2  UNL     1       1.305   2.867  -6.112  1.00  0.00           C  
HETATM    3  C3  UNL     1      -0.009   2.512  -5.448  1.00  0.00           C  
HETATM    4  C4  UNL     1       0.224   2.545  -3.949  1.00  0.00           C  
HETATM    5  C5  UNL     1      -1.093   2.207  -3.267  1.00  0.00           C  
HETATM    6  C6  UNL     1      -0.969   2.218  -1.773  1.00  0.00           C  
HETATM    7  C7  UNL     1      -0.005   1.230  -1.209  1.00  0.00           C  
HETATM    8  C8  UNL     1       0.079   1.310   0.304  1.00  0.00           C  
HETATM    9  C9  UNL     1       0.569   2.671   0.754  1.00  0.00           C  
HETATM   10  C10 UNL     1       1.952   2.965   0.203  1.00  0.00           C  
HETATM   11  C11 UNL     1       2.936   1.920   0.730  1.00  0.00           C  
HETATM   12  C12 UNL     1       4.311   2.172   0.166  1.00  0.00           C  
HETATM   13  C13 UNL     1       5.303   1.180   0.668  1.00  0.00           C  
HETATM   14  C14 UNL     1       5.493   1.215   2.147  1.00  0.00           C  
HETATM   15  C15 UNL     1       6.482   0.243   2.694  1.00  0.00           C  
HETATM   16  C16 UNL     1       6.178  -1.169   2.486  1.00  0.00           C  
HETATM   17  O1  UNL     1       7.039  -2.020   2.900  1.00  0.00           O  
HETATM   18  O2  UNL     1       5.035  -1.639   1.882  1.00  0.00           O  
HETATM   19  C17 UNL     1       4.853  -3.043   1.752  1.00  0.00           C  
HETATM   20  C18 UNL     1       4.641  -3.490   0.344  1.00  0.00           C  
HETATM   21  O3  UNL     1       3.461  -2.925  -0.224  1.00  0.00           O  
HETATM   22  C19 UNL     1       3.110  -3.251  -1.521  1.00  0.00           C  
HETATM   23  O4  UNL     1       3.864  -4.036  -2.149  1.00  0.00           O  
HETATM   24  C20 UNL     1       1.901  -2.733  -2.212  1.00  0.00           C  
HETATM   25  C21 UNL     1       1.807  -3.272  -3.622  1.00  0.00           C  
HETATM   26  C22 UNL     1       0.548  -2.741  -4.308  1.00  0.00           C  
HETATM   27  C23 UNL     1       0.457  -3.251  -5.717  1.00  0.00           C  
HETATM   28  O5  UNL     1       0.409  -4.629  -5.821  1.00  0.00           O  
HETATM   29  C24 UNL     1      -0.568  -2.560  -6.569  1.00  0.00           C  
HETATM   30  O6  UNL     1      -0.535  -1.188  -6.404  1.00  0.00           O  
HETATM   31  C25 UNL     1      -1.878  -3.188  -6.430  1.00  0.00           C  
HETATM   32  C26 UNL     1      -2.803  -2.910  -5.528  1.00  0.00           C  
HETATM   33  C27 UNL     1      -4.060  -3.611  -5.506  1.00  0.00           C  
HETATM   34  C28 UNL     1      -5.046  -3.402  -4.640  1.00  0.00           C  
HETATM   35  C29 UNL     1      -6.241  -4.201  -4.769  1.00  0.00           C  
HETATM   36  C30 UNL     1      -7.255  -4.072  -3.972  1.00  0.00           C  
HETATM   37  C31 UNL     1      -7.271  -3.111  -2.884  1.00  0.00           C  
HETATM   38  C32 UNL     1      -8.331  -3.006  -2.081  1.00  0.00           C  
HETATM   39  C33 UNL     1      -8.546  -2.130  -0.961  1.00  0.00           C  
HETATM   40  O7  UNL     1      -9.897  -1.720  -0.886  1.00  0.00           O  
HETATM   41  C34 UNL     1      -7.628  -0.904  -0.897  1.00  0.00           C  
HETATM   42  C35 UNL     1      -7.981  -0.090   0.310  1.00  0.00           C  
HETATM   43  C36 UNL     1      -7.274   1.168   0.540  1.00  0.00           C  
HETATM   44  C37 UNL     1      -5.803   1.175   0.730  1.00  0.00           C  
HETATM   45  C38 UNL     1      -5.058   0.736  -0.494  1.00  0.00           C  
HETATM   46  C39 UNL     1       3.645  -3.449   2.618  1.00  0.00           C  
HETATM   47  O8  UNL     1       3.867  -3.115   3.944  1.00  0.00           O  
HETATM   48  P1  UNL     1       2.569  -3.521   4.929  1.00  0.00           P  
HETATM   49  O9  UNL     1       2.990  -4.017   6.291  1.00  0.00           O  
HETATM   50  O10 UNL     1       1.686  -4.747   4.133  1.00  0.00           O  
HETATM   51  O11 UNL     1       1.596  -2.150   5.110  1.00  0.00           O  
HETATM   52  P2  UNL     1       2.195  -1.119   6.304  1.00  0.00           P  
HETATM   53  O12 UNL     1       1.315  -1.292   7.527  1.00  0.00           O  
HETATM   54  O13 UNL     1       3.788  -1.506   6.677  1.00  0.00           O  
HETATM   55  O14 UNL     1       2.091   0.488   5.728  1.00  0.00           O  
HETATM   56  C40 UNL     1       2.531   1.288   6.753  1.00  0.00           C  
HETATM   57  C41 UNL     1       2.501   2.731   6.396  1.00  0.00           C  
HETATM   58  O15 UNL     1       3.323   3.042   5.282  1.00  0.00           O  
HETATM   59  C42 UNL     1       2.988   4.411   5.163  1.00  0.00           C  
HETATM   60  N1  UNL     1       3.759   5.077   4.180  1.00  0.00           N  
HETATM   61  C43 UNL     1       5.102   4.833   4.208  1.00  0.00           C  
HETATM   62  C44 UNL     1       5.975   5.396   3.332  1.00  0.00           C  
HETATM   63  C45 UNL     1       5.499   6.257   2.366  1.00  0.00           C  
HETATM   64  N2  UNL     1       6.378   6.864   1.438  1.00  0.00           N  
HETATM   65  N3  UNL     1       4.178   6.482   2.358  1.00  0.00           N  
HETATM   66  C46 UNL     1       3.323   5.914   3.235  1.00  0.00           C  
HETATM   67  O16 UNL     1       2.086   6.154   3.191  1.00  0.00           O  
HETATM   68  C47 UNL     1       1.526   4.370   5.026  1.00  0.00           C  
HETATM   69  O17 UNL     1       0.879   5.543   5.420  1.00  0.00           O  
HETATM   70  C48 UNL     1       1.144   3.269   6.021  1.00  0.00           C  
HETATM   71  O18 UNL     1       0.511   3.841   7.147  1.00  0.00           O  
HETATM   72  H1  UNL     1       0.253   3.286  -7.978  1.00  0.00           H  
HETATM   73  H2  UNL     1       2.088   3.451  -7.989  1.00  0.00           H  
HETATM   74  H3  UNL     1       1.349   1.826  -7.970  1.00  0.00           H  
HETATM   75  H4  UNL     1       1.700   3.832  -5.770  1.00  0.00           H  
HETATM   76  H5  UNL     1       2.040   2.064  -5.834  1.00  0.00           H  
HETATM   77  H6  UNL     1      -0.778   3.239  -5.747  1.00  0.00           H  
HETATM   78  H7  UNL     1      -0.336   1.528  -5.799  1.00  0.00           H  
HETATM   79  H8  UNL     1       0.544   3.548  -3.627  1.00  0.00           H  
HETATM   80  H9  UNL     1       0.970   1.806  -3.645  1.00  0.00           H  
HETATM   81  H10 UNL     1      -1.431   1.196  -3.638  1.00  0.00           H  
HETATM   82  H11 UNL     1      -1.833   2.913  -3.652  1.00  0.00           H  
HETATM   83  H12 UNL     1      -2.002   2.026  -1.369  1.00  0.00           H  
HETATM   84  H13 UNL     1      -0.738   3.256  -1.445  1.00  0.00           H  
HETATM   85  H14 UNL     1       0.996   1.349  -1.677  1.00  0.00           H  
HETATM   86  H15 UNL     1      -0.371   0.206  -1.442  1.00  0.00           H  
HETATM   87  H16 UNL     1       0.702   0.481   0.658  1.00  0.00           H  
HETATM   88  H17 UNL     1      -0.941   1.183   0.684  1.00  0.00           H  
HETATM   89  H18 UNL     1       0.668   2.623   1.865  1.00  0.00           H  
HETATM   90  H19 UNL     1      -0.170   3.441   0.525  1.00  0.00           H  
HETATM   91  H20 UNL     1       1.973   2.972  -0.897  1.00  0.00           H  
HETATM   92  H21 UNL     1       2.279   3.943   0.555  1.00  0.00           H  
HETATM   93  H22 UNL     1       2.618   0.909   0.359  1.00  0.00           H  
HETATM   94  H23 UNL     1       2.918   1.902   1.838  1.00  0.00           H  
HETATM   95  H24 UNL     1       4.220   2.133  -0.940  1.00  0.00           H  
HETATM   96  H25 UNL     1       4.645   3.206   0.441  1.00  0.00           H  
HETATM   97  H26 UNL     1       5.012   0.162   0.299  1.00  0.00           H  
HETATM   98  H27 UNL     1       6.300   1.394   0.207  1.00  0.00           H  
HETATM   99  H28 UNL     1       5.859   2.242   2.437  1.00  0.00           H  
HETATM  100  H29 UNL     1       4.536   1.108   2.716  1.00  0.00           H  
HETATM  101  H30 UNL     1       7.500   0.522   2.282  1.00  0.00           H  
HETATM  102  H31 UNL     1       6.577   0.455   3.785  1.00  0.00           H  
HETATM  103  H32 UNL     1       5.728  -3.546   2.182  1.00  0.00           H  
HETATM  104  H33 UNL     1       4.541  -4.603   0.360  1.00  0.00           H  
HETATM  105  H34 UNL     1       5.510  -3.284  -0.302  1.00  0.00           H  
HETATM  106  H35 UNL     1       1.909  -1.625  -2.281  1.00  0.00           H  
HETATM  107  H36 UNL     1       1.018  -2.990  -1.600  1.00  0.00           H  
HETATM  108  H37 UNL     1       2.698  -3.000  -4.194  1.00  0.00           H  
HETATM  109  H38 UNL     1       1.768  -4.377  -3.526  1.00  0.00           H  
HETATM  110  H39 UNL     1      -0.355  -3.008  -3.747  1.00  0.00           H  
HETATM  111  H40 UNL     1       0.643  -1.638  -4.293  1.00  0.00           H  
HETATM  112  H41 UNL     1       1.463  -2.970  -6.184  1.00  0.00           H  
HETATM  113  H42 UNL     1      -0.438  -4.976  -6.157  1.00  0.00           H  
HETATM  114  H43 UNL     1      -0.236  -2.758  -7.649  1.00  0.00           H  
HETATM  115  H44 UNL     1      -0.967  -1.000  -5.522  1.00  0.00           H  
HETATM  116  H45 UNL     1      -2.145  -3.986  -7.144  1.00  0.00           H  
HETATM  117  H46 UNL     1      -2.568  -2.129  -4.808  1.00  0.00           H  
HETATM  118  H47 UNL     1      -4.211  -4.390  -6.279  1.00  0.00           H  
HETATM  119  H48 UNL     1      -4.907  -2.656  -3.892  1.00  0.00           H  
HETATM  120  H49 UNL     1      -6.306  -4.965  -5.584  1.00  0.00           H  
HETATM  121  H50 UNL     1      -8.123  -4.735  -4.155  1.00  0.00           H  
HETATM  122  H51 UNL     1      -6.463  -2.440  -2.655  1.00  0.00           H  
HETATM  123  H52 UNL     1      -9.144  -3.711  -2.348  1.00  0.00           H  
HETATM  124  H53 UNL     1      -8.367  -2.690  -0.014  1.00  0.00           H  
HETATM  125  H54 UNL     1     -10.478  -2.285  -1.439  1.00  0.00           H  
HETATM  126  H55 UNL     1      -7.789  -0.326  -1.815  1.00  0.00           H  
HETATM  127  H56 UNL     1      -6.578  -1.259  -0.827  1.00  0.00           H  
HETATM  128  H57 UNL     1      -9.098   0.163   0.299  1.00  0.00           H  
HETATM  129  H58 UNL     1      -7.946  -0.777   1.229  1.00  0.00           H  
HETATM  130  H59 UNL     1      -7.450   1.809  -0.403  1.00  0.00           H  
HETATM  131  H60 UNL     1      -7.785   1.807   1.337  1.00  0.00           H  
HETATM  132  H61 UNL     1      -5.490   2.225   0.982  1.00  0.00           H  
HETATM  133  H62 UNL     1      -5.565   0.504   1.602  1.00  0.00           H  
HETATM  134  H63 UNL     1      -4.577  -0.257  -0.395  1.00  0.00           H  
HETATM  135  H64 UNL     1      -5.686   0.748  -1.402  1.00  0.00           H  
HETATM  136  H65 UNL     1      -4.235   1.502  -0.675  1.00  0.00           H  
HETATM  137  H66 UNL     1       2.735  -2.943   2.193  1.00  0.00           H  
HETATM  138  H67 UNL     1       3.486  -4.539   2.519  1.00  0.00           H  
HETATM  139  H68 UNL     1       0.773  -4.468   3.923  1.00  0.00           H  
HETATM  140  H69 UNL     1       4.100  -0.984   7.456  1.00  0.00           H  
HETATM  141  H70 UNL     1       1.979   1.166   7.701  1.00  0.00           H  
HETATM  142  H71 UNL     1       3.599   1.018   6.931  1.00  0.00           H  
HETATM  143  H72 UNL     1       2.906   3.370   7.230  1.00  0.00           H  
HETATM  144  H73 UNL     1       3.242   4.836   6.155  1.00  0.00           H  
HETATM  145  H74 UNL     1       5.533   4.152   4.958  1.00  0.00           H  
HETATM  146  H75 UNL     1       7.039   5.185   3.375  1.00  0.00           H  
HETATM  147  H76 UNL     1       7.172   7.443   1.755  1.00  0.00           H  
HETATM  148  H77 UNL     1       6.241   6.739   0.416  1.00  0.00           H  
HETATM  149  H78 UNL     1       1.155   4.004   4.045  1.00  0.00           H  
HETATM  150  H79 UNL     1       1.456   6.140   5.949  1.00  0.00           H  
HETATM  151  H80 UNL     1       0.478   2.515   5.571  1.00  0.00           H  
HETATM  152  H81 UNL     1      -0.350   4.236   6.802  1.00  0.00           H  
CONECT    1    2   72   73   74
CONECT    2    3   75   76
CONECT    3    4   77   78
CONECT    4    5   79   80
CONECT    5    6   81   82
CONECT    6    7   83   84
CONECT    7    8   85   86
CONECT    8    9   87   88
CONECT    9   10   89   90
CONECT   10   11   91   92
CONECT   11   12   93   94
CONECT   12   13   95   96
CONECT   13   14   97   98
CONECT   14   15   99  100
CONECT   15   16  101  102
CONECT   16   17   17   18
CONECT   18   19
CONECT   19   20   46  103
CONECT   20   21  104  105
CONECT   21   22
CONECT   22   23   23   24
CONECT   24   25  106  107
CONECT   25   26  108  109
CONECT   26   27  110  111
CONECT   27   28   29  112
CONECT   28  113
CONECT   29   30   31  114
CONECT   30  115
CONECT   31   32   32  116
CONECT   32   33  117
CONECT   33   34   34  118
CONECT   34   35  119
CONECT   35   36   36  120
CONECT   36   37  121
CONECT   37   38   38  122
CONECT   38   39  123
CONECT   39   40   41  124
CONECT   40  125
CONECT   41   42  126  127
CONECT   42   43  128  129
CONECT   43   44  130  131
CONECT   44   45  132  133
CONECT   45  134  135  136
CONECT   46   47  137  138
CONECT   47   48
CONECT   48   49   49   50   51
CONECT   50  139
CONECT   51   52
CONECT   52   53   53   54   55
CONECT   54  140
CONECT   55   56
CONECT   56   57  141  142
CONECT   57   58   70  143
CONECT   58   59
CONECT   59   60   68  144
CONECT   60   61   66
CONECT   61   62   62  145
CONECT   62   63  146
CONECT   63   64   65   65
CONECT   64  147  148
CONECT   65   66
CONECT   66   67   67
CONECT   68   69   70  149
CONECT   69  150
CONECT   70   71  151
CONECT   71  152
END
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SMILES for HMDB0290805 (CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0))

[H][C@@](COC(=O)CCC[C@@H](O)[C@H](O)\C=C\C=C\C=C/C=C/[C@H](O)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)CCCCCCCCCCCCCCC
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INCHI for HMDB0290805 (CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0))

InChI=1S/C48H81N3O18P2/c1-3-5-7-8-9-10-11-12-13-14-15-20-24-30-44(56)67-38(34-64-43(55)31-25-29-40(54)39(53)28-23-19-17-16-18-22-27-37(52)26-21-6-4-2)35-65-70(60,61)69-71(62,63)66-36-41-45(57)46(58)47(68-41)51-33-32-42(49)50-48(51)59/h16-19,22-23,27-28,32-33,37-41,45-47,52-54,57-58H,3-15,20-21,24-26,29-31,34-36H2,1-2H3,(H,60,61)(H,62,63)(H2,49,50,59)/b18-16-,19-17+,27-22+,28-23+/t37-,38-,39-,40-,41-,45-,46-,47-/m1/s1
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View in JSmolView Stereo Labels
Synonyms
ValueSource
{[(2R,3S,4R,5R)-3,4-dihydroxy-5-(2-hydroxy-4-imino-1,4-dihydropyrimidin-1-yl)oxolan-2-yl]methoxy}({[(2R)-2-(hexadecanoyloxy)-3-{[(5R,6R,7E,9E,11Z,15R)-5,6,15-trihydroxyicosa-7,9,11,13-tetraenoyl]oxy}propoxy](hydroxy)phosphoryl}oxy)phosphinateGenerator
Chemical FormulaC48H81N3O18P2
Average Molecular Weight1050.127
Monoisotopic Molecular Weight1049.499036776
IUPAC Name{[(2R,3S,4R,5R)-5-(4-amino-2-oxo-1,2-dihydropyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}({[(2R)-2-(hexadecanoyloxy)-3-{[(5R,6R,7E,9E,11Z,13E,15R)-5,6,15-trihydroxyicosa-7,9,11,13-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)-2-(hexadecanoyloxy)-3-{[(5R,6R,7E,9E,11Z,13E,15R)-5,6,15-trihydroxyicosa-7,9,11,13-tetraenoyl]oxy}propoxy(hydroxy)phosphoryl]oxy)phosphinic acid
CAS Registry NumberNot Available
SMILES
[H][C@@](COC(=O)CCC[C@@H](O)[C@H](O)\C=C\C=C\C=C/C=C/[C@H](O)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)CCCCCCCCCCCCCCC
InChI Identifier
InChI=1S/C48H81N3O18P2/c1-3-5-7-8-9-10-11-12-13-14-15-20-24-30-44(56)67-38(34-64-43(55)31-25-29-40(54)39(53)28-23-19-17-16-18-22-27-37(52)26-21-6-4-2)35-65-70(60,61)69-71(62,63)66-36-41-45(57)46(58)47(68-41)51-33-32-42(49)50-48(51)59/h16-19,22-23,27-28,32-33,37-41,45-47,52-54,57-58H,3-15,20-21,24-26,29-31,34-36H2,1-2H3,(H,60,61)(H,62,63)(H2,49,50,59)/b18-16-,19-17+,27-22+,28-23+/t37-,38-,39-,40-,41-,45-,46-,47-/m1/s1
InChI KeyZYNASFISMGAGIS-VEDJJGNASA-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
logP4.76ALOGPS
logP6.35ChemAxon
logS-5ALOGPS
pKa (Strongest Acidic)-0.02ChemAxon
pKa (Strongest Basic)3.27ChemAxon
Physiological Charge-2ChemAxon
Hydrogen Acceptor Count15ChemAxon
Hydrogen Donor Count8ChemAxon
Polar Surface Area323.96 ŲChemAxon
Rotatable Bond Count42ChemAxon
Refractivity267.47 m³·mol⁻¹ChemAxon
Polarizability112.01 ųChemAxon
Number of Rings2ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleNoChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+316.32632859911
AllCCS[M+H-H2O]+316.81732859911
AllCCS[M+Na]+315.68832859911
AllCCS[M+NH4]+315.83532859911
AllCCS[M-H]-314.92732859911
AllCCS[M+Na-2H]-321.3332859911
AllCCS[M+HCOO]-328.29332859911
DeepCCS[M+H]+283.08830932474
DeepCCS[M-H]-280.46230932474
DeepCCS[M-2H]-315.84130932474
DeepCCS[M+Na]+290.25230932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0) 10V, Positive-QTOFsplash10-03di-9000000003-7a082a86759238e8595f2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0) 20V, Positive-QTOFsplash10-03di-4110000019-56a05e94a0fb32b10c7f2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0) 40V, Positive-QTOFsplash10-0002-0019002200-0e7b42ed694b0f7d90fd2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0) 10V, Negative-QTOFsplash10-0002-9000000100-0c0d07aba2d0fb6ae8722021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0) 20V, Negative-QTOFsplash10-004i-6022210900-ba5a39aaac60235121de2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - CDP-DG(20:4(7E,9E,11Z,13E)-3OH(5S,6R,15S)/16:0) 40V, Negative-QTOFsplash10-05o9-2369403320-600c0c1e92475aff2f082021-10-21Wishart 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 ]