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Showing metabocard for (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA (HMDB0301546)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-22 00:53:20 UTC
Update Date2021-10-01 16:54:59 UTC
HMDB IDHMDB0301546
Secondary Accession NumbersNone
Metabolite Identification
Common Name(5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA
Description(5z)-7-[(1r,2e)-2-[(3s)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-coa is an acyl-CoA or acyl-coenzyme A. More specifically, it is a (5Z)-7-[(1R_2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoic acid thioester of coenzyme A. (5z)-7-[(1r,2e)-2-[(3s)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-coa is an acyl-CoA with 20 fatty acid group as the acyl moiety attached to coenzyme A. Coenzyme A was discovered in 1946 by Fritz Lipmann (Journal of Biological Chemistry (1946) 162 (3): 743–744) and its structure was determined in the early 1950s at the Lister Institute in London. Coenzyme A is a complex, thiol-containing molecule that is naturally synthesized from pantothenate (vitamin B5), which is found in various foods such as meat, vegetables, cereal grains, legumes, eggs, and milk. More specifically, coenzyme A (CoASH or CoA) consists of a beta-mercaptoethylamine group linked to the vitamin pantothenic acid (B5) through an amide linkage and 3'-phosphorylated ADP. Coenzyme A is synthesized in a five-step process that requires four molecules of ATP, pantothenate and cysteine. It is believed that there are more than 1100 types of acyl-CoA’s in the human body, which also corresponds to the number of acylcarnitines in the human body. Acyl-CoAs exists in all living species, ranging from bacteria to plants to humans. The general role of acyl-CoA’s is to assist in transferring fatty acids from the cytoplasm to mitochondria. This process facilitates the production of fatty acids in cells, which are essential in cell membrane structure. Acyl-CoA's are also susceptible to beta oxidation, forming, ultimately, acetyl-CoA. Acetyl-CoA can enter the citric acid cycle, eventually forming several equivalents of ATP. In this way, fats are converted to ATP -- or biochemical energy. Acyl-CoAs can be classified into 9 different categories depending on the size of their acyl-group: 1) short-chain acyl-CoAs; 2) medium-chain acyl-CoAs; 3) long-chain acyl-CoAs; and 4) very long-chain acyl-CoAs; 5) hydroxy acyl-CoAs; 6) branched chain acyl-CoAs; 7) unsaturated acyl-CoAs; 8) dicarboxylic acyl-CoAs and 9) miscellaneous acyl-CoAs. Short-chain acyl-CoAs have acyl-groups with two to four carbons (C2-C4), medium-chain acyl-CoAs have acyl-groups with five to eleven carbons (C5-C11), long-chain acyl-CoAs have acyl-groups with twelve to twenty carbons (C12-C20) while very long-chain acyl-CoAs have acyl groups with more than 20 carbons. (5z)-7-[(1r,2e)-2-[(3s)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-coa is therefore classified as a long chain acyl-CoA. The oxidative degradation of fatty acids is a two-step process, catalyzed by acyl-CoA synthetase/synthase. Fatty acids are first converted to their acyl phosphate, the precursor to acyl-CoA. The latter conversion is mediated by acyl-CoA synthase. Three types of acyl-CoA synthases are employed, depending on the chain length of the fatty acid. (5z)-7-[(1r,2e)-2-[(3s)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-coa, being a long chain acyl-CoA is a substrate for long chain acyl-CoA synthase. The second step of fatty acid degradation is beta oxidation. Beta oxidation occurs in mitochondria and, in the case of very long chain acyl-CoAs, the peroxisome. After its formation in the cytosol, (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA is transported into the mitochondria, the locus of beta oxidation. Transport of (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA into the mitochondria requires carnitine palmitoyltransferase 1 (CPT1), which converts (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA into (5Z)-7-[(1R_2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoylcarnitine, which gets transported into the mitochondrial matrix. Once in the matrix, (5Z)-7-[(1R_2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoylcarnitine is converted back to (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA by CPT2, whereupon beta-oxidation can begin. Beta oxidation of (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA occurs in four steps. First, since (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA is a long chain acyl-CoA it is the substrate for a long chain acyl-CoA dehydrogenase, which catalyzes dehydrogenation of (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA, creating a double bond between the alpha and beta carbons. FAD is the hydrogen acceptor, yielding FADH2. Second, Enoyl-CoA hydrase catalyzes the addition of water across the newly formed double bond to make an alcohol. Third, 3-hydroxyacyl-CoA dehydrogenase oxidizes the alcohol group to a ketone and NADH is produced from NAD+. Finally, Thiolase cleaves between the alpha carbon and ketone to release one molecule of acetyl-CoA and a new acyl-CoA which is now 2 carbons shorter. This four-step process repeats until (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA has had all its carbons removed from the chain, leaving only acetyl-CoA. Beta oxidation, as well as alpha-oxidation, also occurs in the peroxisome. The peroxisome handles beta oxidation of fatty acids that have more than 20 carbons in their chain because the peroxisome contains very-long-chain Acyl-CoA synthetases and dehydrogenases. The heart primarily metabolizes fat for energy and Acyl-CoA metabolism has been identified as a critical molecule in early-stage heart muscle pump failure. Cellular acyl-CoA content also correlates with insulin resistance, suggesting that it can mediate lipotoxicity in non-adipose tissues. Acyl-CoA: diacylglycerol acyltransferase (DGAT) plays an important role in energy metabolism on account of key enzyme in triglyceride biosynthesis. The study of acyl-CoAs is an active area of research and it is likely that many novel acyl-CoAs will be discovered in the coming years. It is also likely that many novel roles in health and disease will be uncovered for these molecules.
Structure
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MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for HMDB0301546 ((5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA)


  Mrv1652304102105332D          

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M  END
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3D MOL for HMDB0301546 ((5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA)

HMDB0301546
     RDKit          3D
(5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA
137140  0  0  0  0  0  0  0  0999 V2000
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M  END
Download

3D SDF for HMDB0301546 ((5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA)


  Mrv1652304102105332D          

 71 74  0  0  0  0            999 V2000
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   23.9237   -4.1077    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5258   -3.0909    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.1903   -3.8445    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.1133   -2.3764    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.6654   -1.7633    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
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  7  9  1  0  0  0  0
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 57 71  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0301546

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCC(O)CC=C1C(CC=CCCCC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2OP(O)(O)=O)N2C=NC3=C2N=CN=C3N)CCC1=O

> <INCHI_IDENTIFIER>
InChI=1S/C41H66N7O19P3S/c1-4-5-8-12-27(49)15-16-28-26(14-17-29(28)50)11-9-6-7-10-13-32(52)71-21-20-43-31(51)18-19-44-39(55)36(54)41(2,3)23-64-70(61,62)67-69(59,60)63-22-30-35(66-68(56,57)58)34(53)40(65-30)48-25-47-33-37(42)45-24-46-38(33)48/h6,9,16,24-27,30,34-36,40,49,53-54H,4-5,7-8,10-15,17-23H2,1-3H3,(H,43,51)(H,44,55)(H,59,60)(H,61,62)(H2,42,45,46)(H2,56,57,58)

> <INCHI_KEY>
NYGXGWCQLFQCML-UHFFFAOYSA-N

> <FORMULA>
C41H66N7O19P3S

> <MOLECULAR_WEIGHT>
1085.99

> <EXACT_MASS>
1085.334705101

> <JCHEM_ACCEPTOR_COUNT>
19

> <JCHEM_ATOM_COUNT>
137

> <JCHEM_AVERAGE_POLARIZABILITY>
108.0319714542352

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-({[hydroxy({[hydroxy({3-hydroxy-3-[(2-{[2-({7-[2-(3-hydroxyoctylidene)-3-oxocyclopentyl]hept-5-enoyl}sulfanyl)ethyl]carbamoyl}ethyl)carbamoyl]-2,2-dimethylpropoxy})phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-3-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
1.84

> <JCHEM_LOGP>
-1.223744027481295

> <ALOGPS_LOGS>
-2.94

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
4

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.900120734776186

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.820978781339821

> <JCHEM_PKA_STRONGEST_BASIC>
4.006053268556904

> <JCHEM_POLAR_SURFACE_AREA>
400.93

> <JCHEM_REFRACTIVITY>
257.47420000000005

> <JCHEM_ROTATABLE_BOND_COUNT>
32

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.25e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[5-(6-aminopurin-9-yl)-4-hydroxy-2-({[hydroxy([hydroxy(3-hydroxy-3-[(2-{[2-({7-[2-(3-hydroxyoctylidene)-3-oxocyclopentyl]hept-5-enoyl}sulfanyl)ethyl]carbamoyl}ethyl)carbamoyl]-2,2-dimethylpropoxy)phosphoryl]oxy)phosphoryl]oxy}methyl)oxolan-3-yl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0301546 ((5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA)

HMDB0301546
     RDKit          3D
(5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA
137140  0  0  0  0  0  0  0  0999 V2000
   18.2886   -1.0396   -0.5202 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.2676   -0.6748   -1.5769 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.9135   -0.6072   -0.9094 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.8990   -0.2349   -1.9842 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5608   -0.1637   -1.2777 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.4409    0.1945   -2.2456 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.2756   -0.7141   -3.2584 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.1990    0.3850   -1.4308 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7994   -0.8206   -0.6709 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.7495   -0.8619    0.6364 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.3738   -1.9785    1.5056 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6079   -2.9191    1.1314 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.0280   -1.7852    2.8055 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.7006   -0.4688    2.7630 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.1003    0.2474    1.5515 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8616    0.9463    2.0217 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.0611    1.5249    0.9395 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.8053    1.1892    0.7171 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9833    0.2391    1.4377 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.8205    0.8344    2.1446 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9062    1.6132    1.2852 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4218    2.8758    0.7472 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.3879    3.3614    1.3977 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8871    3.7775   -0.6418 S   0  0  0  0  0  0  0  0  0  0  0  0
    3.3894    3.2978   -1.4367 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1181    3.5330   -0.7101 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8385    2.8177    0.4725 N   0  0  0  0  0  0  0  0  0  0  0  0
    1.6388    1.3799    0.4612 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7272    0.8100   -0.6503 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3482    0.6388    1.6654 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4224   -0.5132    1.5376 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9357   -0.2494    1.2871 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5858    0.3796    0.2260 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0667    0.8617   -0.7979 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0899    0.5318    0.2576 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5785   -0.0299    1.4095 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7299    0.0079   -1.0032 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4050   -1.4588   -1.1468 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.1935    0.8091   -2.1841 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2390    0.1592   -0.9165 C   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7593   -0.5344    0.1481 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.4304   -0.3485    0.2895 P   0  0  0  0  0  5  0  0  0  0  0  0
   -7.7586    0.9912   -0.3764 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.8815   -0.1732    1.9120 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2433   -1.5811   -0.4828 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.6062   -2.8931    0.4935 P   0  0  0  0  0  5  0  0  0  0  0  0
   -7.9045   -2.8077    1.8282 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1389   -4.3163   -0.3277 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2690   -2.9916    0.7580 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8266   -1.7699    1.0977 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3130   -1.8680    1.3459 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.8628   -0.6568    1.6730 O   0  0  0  0  0  0  0  0  0  0  0  0
  -13.9800   -0.4231    0.9082 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.2216    0.9969    0.7637 N   0  0  0  0  0  0  0  0  0  0  0  0
  -13.4273    2.0314    1.0606 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.0382    3.1946    0.7689 N   0  0  0  0  0  0  0  0  0  0  0  0
  -15.2587    2.9056    0.2708 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.2984    3.7138   -0.1871 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.1182    5.1084   -0.1586 N   0  0  0  0  0  0  0  0  0  0  0  0
  -17.4157    3.1176   -0.6315 N   0  0  0  0  0  0  0  0  0  0  0  0
  -17.5190    1.7799   -0.6310 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5174    1.0019   -0.1899 N   0  0  0  0  0  0  0  0  0  0  0  0
  -15.3550    1.5347    0.2752 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6387   -1.1013   -0.4039 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.7918   -1.3828   -1.1354 O   0  0  0  0  0  0  0  0  0  0  0  0
  -13.0016   -2.3981    0.1226 C   0  0  0  0  0  0  0  0  0  0  0  0
  -14.0519   -3.2399    0.4182 O   0  0  0  0  0  0  0  0  0  0  0  0
  -14.0646   -4.6873   -0.4058 P   0  0  0  0  0  5  0  0  0  0  0  0
  -15.0492   -5.6625    0.2462 O   0  0  0  0  0  0  0  0  0  0  0  0
  -14.6285   -4.4170   -1.9763 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.5352   -5.4016   -0.5367 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.1619   -0.3265   -0.6204 H   0  0  0  0  0  0  0  0  0  0  0  0
   18.6768   -2.0632   -0.6240 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.8662   -0.8118    0.4756 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.2205   -1.4302   -2.3607 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.5224    0.3316   -2.0198 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.8845    0.0956   -0.0659 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.6990   -1.6374   -0.5205 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.9454   -0.9710   -2.7835 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.1518    0.7655   -2.4146 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.3935   -1.1555   -0.8217 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.5830    0.5757   -0.4610 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.6732    1.1887   -2.7076 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.5225   -1.6395   -3.0267 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.3701    1.2631   -0.7786 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.3232    0.6895   -2.0808 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.5253   -1.7416   -1.2181 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2628   -1.8203    3.6406 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7609   -2.6069    2.9941 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4212    0.1224    3.6767 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7977   -0.5040    2.6293 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.8220    0.9528    1.1340 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2016    1.8145    2.6600 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3101    0.2654    2.7025 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5316    2.2635    0.3083 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.3455    1.6610   -0.1691 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.5270   -0.4872    0.6762 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5683   -0.4474    2.1061 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.2312    1.5132    2.9668 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.2757    0.0540    2.7446 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.0195    1.8881    1.9401 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4585    0.9880    0.4565 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3221    3.8595   -2.4182 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4383    2.2147   -1.7804 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0430    4.6323   -0.4897 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2711    3.3366   -1.4384 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.7705    3.3259    1.3937 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.9432    1.3745    2.4188 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3288    0.2874    2.0970 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7992   -1.2091    0.7023 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5942   -1.1631    2.4444 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5884   -0.6223    2.1070 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.3374    1.6297    0.3060 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7182   -1.0104    1.3308 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.7153   -1.8431   -2.1558 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0103   -2.0216   -0.4071 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3116   -1.5630   -0.9952 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8546    1.8105   -1.9241 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3526    0.2466   -2.6298 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9585    0.8963   -2.9870 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.5143    1.2431   -0.8694 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.7127   -0.2224   -1.8439 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.0890   -0.1343    2.4815 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.7083   -4.0979   -1.1990 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.5784   -0.9861    0.3591 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2896   -1.4513    2.0396 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4318   -2.5333    2.2278 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.8443   -0.8976    1.4184 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4370    1.9332    1.4768 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.5660    5.5764    0.5801 H   0  0  0  0  0  0  0  0  0  0  0  0
  -16.5505    5.6930   -0.8995 H   0  0  0  0  0  0  0  0  0  0  0  0
  -18.4476    1.3698   -1.0029 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.9159   -0.4936   -0.9464 H   0  0  0  0  0  0  0  0  0  0  0  0
  -14.5273   -1.6660   -2.0266 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3134   -2.7461   -0.6423 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.9311   -4.4212   -2.6523 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.9522   -4.7544   -0.9977 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
  6  8  1  0
  8  9  1  0
  9 10  2  3
 10 11  1  0
 11 12  2  0
 11 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  2  3
 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
 28 29  2  0
 28 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  1  0
 33 34  2  0
 33 35  1  0
 35 36  1  0
 35 37  1  0
 37 38  1  0
 37 39  1  0
 37 40  1  0
 40 41  1  0
 41 42  1  0
 42 43  2  0
 42 44  1  0
 42 45  1  0
 45 46  1  0
 46 47  2  0
 46 48  1  0
 46 49  1  0
 49 50  1  0
 50 51  1  0
 51 52  1  0
 52 53  1  0
 53 54  1  0
 54 55  1  0
 55 56  2  0
 56 57  1  0
 57 58  2  0
 58 59  1  0
 58 60  1  0
 60 61  2  0
 61 62  1  0
 62 63  2  0
 53 64  1  0
 64 65  1  0
 64 66  1  0
 66 67  1  0
 67 68  1  0
 68 69  2  0
 68 70  1  0
 68 71  1  0
 15 10  1  0
 66 51  1  0
 63 54  1  0
 63 57  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
  7 84  1  0
  8 85  1  0
  8 86  1  0
  9 87  1  0
 13 88  1  0
 13 89  1  0
 14 90  1  0
 14 91  1  0
 15 92  1  0
 16 93  1  0
 16 94  1  0
 17 95  1  0
 18 96  1  0
 19 97  1  0
 19 98  1  0
 20 99  1  0
 20100  1  0
 21101  1  0
 21102  1  0
 25103  1  0
 25104  1  0
 26105  1  0
 26106  1  0
 27107  1  0
 30108  1  0
 30109  1  0
 31110  1  0
 31111  1  0
 32112  1  0
 35113  1  0
 36114  1  0
 38115  1  0
 38116  1  0
 38117  1  0
 39118  1  0
 39119  1  0
 39120  1  0
 40121  1  0
 40122  1  0
 44123  1  0
 48124  1  0
 50125  1  0
 50126  1  0
 51127  1  0
 53128  1  0
 55129  1  0
 59130  1  0
 59131  1  0
 61132  1  0
 64133  1  0
 65134  1  0
 66135  1  0
 70136  1  0
 71137  1  0
M  END
Download

PDB for HMDB0301546 ((5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA)

HEADER    PROTEIN                                 10-APR-21   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-APR-21         0                                  
HETATM    1  O   UNK     0      33.049   3.012   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      33.049   1.472   0.000  0.00  0.00           C+0
HETATM    3  S   UNK     0      31.715   0.702   0.000  0.00  0.00           S+0
HETATM    4  C   UNK     0      30.381   1.472   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      29.047   0.702   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      27.714   1.472   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      26.380   0.702   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      26.380  -0.838   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      25.046   1.472   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      23.713   0.702   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      22.379   1.472   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      21.045   0.702   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      21.045  -0.838   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      19.712   1.472   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      19.712   3.012   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      18.378   0.702   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      19.148  -0.632   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      17.608   2.036   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      17.044  -0.068   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      15.711   0.702   0.000  0.00  0.00           O+0
HETATM   21  P   UNK     0      14.377  -0.068   0.000  0.00  0.00           P+0
HETATM   22  O   UNK     0      15.147  -1.402   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0      13.607   1.266   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      13.043  -0.838   0.000  0.00  0.00           O+0
HETATM   25  P   UNK     0      11.710  -0.068   0.000  0.00  0.00           P+0
HETATM   26  O   UNK     0      10.940  -1.402   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0      12.480   1.266   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0      10.376   0.702   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       9.042  -0.068   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       7.709   0.702   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       6.302   0.076   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0       5.271   1.220   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0       3.740   1.059   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0       2.970  -0.274   0.000  0.00  0.00           C+0
HETATM   35  N   UNK     0       1.463   0.046   0.000  0.00  0.00           N+0
HETATM   36  C   UNK     0       1.302   1.577   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0       0.057   2.483   0.000  0.00  0.00           C+0
HETATM   38  N   UNK     0       0.217   4.014   0.000  0.00  0.00           N+0
HETATM   39  C   UNK     0       1.624   4.640   0.000  0.00  0.00           C+0
HETATM   40  N   UNK     0       2.870   3.735   0.000  0.00  0.00           N+0
HETATM   41  C   UNK     0       2.709   2.204   0.000  0.00  0.00           C+0
HETATM   42  N   UNK     0      -1.350   1.856   0.000  0.00  0.00           N+0
HETATM   43  C   UNK     0       6.041   2.554   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0       5.415   3.961   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0       7.548   2.234   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0       8.692   3.264   0.000  0.00  0.00           O+0
HETATM   47  P   UNK     0      10.157   2.788   0.000  0.00  0.00           P+0
HETATM   48  O   UNK     0       9.681   1.324   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      10.633   4.253   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      11.621   2.312   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      34.382   0.702   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      35.716   1.472   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      37.050   0.702   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      37.050  -0.838   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      35.716  -1.608   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      35.716  -3.148   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      34.382  -3.918   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      34.221  -5.449   0.000  0.00  0.00           C+0
HETATM   59  C   UNK     0      35.366  -6.480   0.000  0.00  0.00           C+0
HETATM   60  C   UNK     0      36.830  -6.004   0.000  0.00  0.00           C+0
HETATM   61  C   UNK     0      37.975  -7.034   0.000  0.00  0.00           C+0
HETATM   62  O   UNK     0      37.655  -8.541   0.000  0.00  0.00           O+0
HETATM   63  C   UNK     0      39.439  -6.559   0.000  0.00  0.00           C+0
HETATM   64  C   UNK     0      40.584  -7.589   0.000  0.00  0.00           C+0
HETATM   65  C   UNK     0      42.048  -7.113   0.000  0.00  0.00           C+0
HETATM   66  C   UNK     0      43.193  -8.144   0.000  0.00  0.00           C+0
HETATM   67  C   UNK     0      44.657  -7.668   0.000  0.00  0.00           C+0
HETATM   68  C   UNK     0      32.715  -5.770   0.000  0.00  0.00           C+0
HETATM   69  O   UNK     0      32.088  -7.176   0.000  0.00  0.00           O+0
HETATM   70  C   UNK     0      31.945  -4.436   0.000  0.00  0.00           C+0
HETATM   71  C   UNK     0      32.975  -3.291   0.000  0.00  0.00           C+0
CONECT    1    2                                                            
CONECT    2    1    3   51                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12                                                       
CONECT   12   11   13   14                                                  
CONECT   13   12                                                            
CONECT   14   12   15   16                                                  
CONECT   15   14                                                            
CONECT   16   14   17   18   19                                             
CONECT   17   16                                                            
CONECT   18   16                                                            
CONECT   19   16   20                                                       
CONECT   20   19   21                                                       
CONECT   21   20   22   23   24                                             
CONECT   22   21                                                            
CONECT   23   21                                                            
CONECT   24   21   25                                                       
CONECT   25   24   26   27   28                                             
CONECT   26   25                                                            
CONECT   27   25                                                            
CONECT   28   25   29                                                       
CONECT   29   28   30                                                       
CONECT   30   29   31   45                                                  
CONECT   31   30   32                                                       
CONECT   32   31   33   43                                                  
CONECT   33   32   34   41                                                  
CONECT   34   33   35                                                       
CONECT   35   34   36                                                       
CONECT   36   35   37   41                                                  
CONECT   37   36   38   42                                                  
CONECT   38   37   39                                                       
CONECT   39   38   40                                                       
CONECT   40   39   41                                                       
CONECT   41   40   36   33                                                  
CONECT   42   37                                                            
CONECT   43   32   44   45                                                  
CONECT   44   43                                                            
CONECT   45   43   30   46                                                  
CONECT   46   45   47                                                       
CONECT   47   46   48   49   50                                             
CONECT   48   47                                                            
CONECT   49   47                                                            
CONECT   50   47                                                            
CONECT   51    2   52                                                       
CONECT   52   51   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58   71                                                  
CONECT   58   57   59   68                                                  
CONECT   59   58   60                                                       
CONECT   60   59   61                                                       
CONECT   61   60   62   63                                                  
CONECT   62   61                                                            
CONECT   63   61   64                                                       
CONECT   64   63   65                                                       
CONECT   65   64   66                                                       
CONECT   66   65   67                                                       
CONECT   67   66                                                            
CONECT   68   58   69   70                                                  
CONECT   69   68                                                            
CONECT   70   68   71                                                       
CONECT   71   70   57                                                       
MASTER        0    0    0    0    0    0    0    0   71    0  148    0
END
Download

3D PDB for HMDB0301546 ((5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA)

COMPND    HMDB0301546
HETATM    1  C1  UNL     1      18.289  -1.040  -0.520  1.00  0.00           C  
HETATM    2  C2  UNL     1      17.268  -0.675  -1.577  1.00  0.00           C  
HETATM    3  C3  UNL     1      15.913  -0.607  -0.909  1.00  0.00           C  
HETATM    4  C4  UNL     1      14.899  -0.235  -1.984  1.00  0.00           C  
HETATM    5  C5  UNL     1      13.561  -0.164  -1.278  1.00  0.00           C  
HETATM    6  C6  UNL     1      12.441   0.194  -2.246  1.00  0.00           C  
HETATM    7  O1  UNL     1      12.276  -0.714  -3.258  1.00  0.00           O  
HETATM    8  C7  UNL     1      11.199   0.385  -1.431  1.00  0.00           C  
HETATM    9  C8  UNL     1      10.799  -0.821  -0.671  1.00  0.00           C  
HETATM   10  C9  UNL     1      10.749  -0.862   0.636  1.00  0.00           C  
HETATM   11  C10 UNL     1      10.374  -1.979   1.506  1.00  0.00           C  
HETATM   12  O2  UNL     1       9.608  -2.919   1.131  1.00  0.00           O  
HETATM   13  C11 UNL     1      11.028  -1.785   2.805  1.00  0.00           C  
HETATM   14  C12 UNL     1      11.701  -0.469   2.763  1.00  0.00           C  
HETATM   15  C13 UNL     1      11.100   0.247   1.552  1.00  0.00           C  
HETATM   16  C14 UNL     1       9.862   0.946   2.022  1.00  0.00           C  
HETATM   17  C15 UNL     1       9.061   1.525   0.940  1.00  0.00           C  
HETATM   18  C16 UNL     1       7.805   1.189   0.717  1.00  0.00           C  
HETATM   19  C17 UNL     1       6.983   0.239   1.438  1.00  0.00           C  
HETATM   20  C18 UNL     1       5.820   0.834   2.145  1.00  0.00           C  
HETATM   21  C19 UNL     1       4.906   1.613   1.285  1.00  0.00           C  
HETATM   22  C20 UNL     1       5.422   2.876   0.747  1.00  0.00           C  
HETATM   23  O3  UNL     1       6.388   3.361   1.398  1.00  0.00           O  
HETATM   24  S1  UNL     1       4.887   3.777  -0.642  1.00  0.00           S  
HETATM   25  C21 UNL     1       3.389   3.298  -1.437  1.00  0.00           C  
HETATM   26  C22 UNL     1       2.118   3.533  -0.710  1.00  0.00           C  
HETATM   27  N1  UNL     1       1.838   2.818   0.472  1.00  0.00           N  
HETATM   28  C23 UNL     1       1.639   1.380   0.461  1.00  0.00           C  
HETATM   29  O4  UNL     1       1.727   0.810  -0.650  1.00  0.00           O  
HETATM   30  C24 UNL     1       1.348   0.639   1.665  1.00  0.00           C  
HETATM   31  C25 UNL     1       0.422  -0.513   1.538  1.00  0.00           C  
HETATM   32  N2  UNL     1      -0.936  -0.249   1.287  1.00  0.00           N  
HETATM   33  C26 UNL     1      -1.586   0.380   0.226  1.00  0.00           C  
HETATM   34  O5  UNL     1      -1.067   0.862  -0.798  1.00  0.00           O  
HETATM   35  C27 UNL     1      -3.090   0.532   0.258  1.00  0.00           C  
HETATM   36  O6  UNL     1      -3.579  -0.030   1.409  1.00  0.00           O  
HETATM   37  C28 UNL     1      -3.730   0.008  -1.003  1.00  0.00           C  
HETATM   38  C29 UNL     1      -3.405  -1.459  -1.147  1.00  0.00           C  
HETATM   39  C30 UNL     1      -3.193   0.809  -2.184  1.00  0.00           C  
HETATM   40  C31 UNL     1      -5.239   0.159  -0.916  1.00  0.00           C  
HETATM   41  O7  UNL     1      -5.759  -0.534   0.148  1.00  0.00           O  
HETATM   42  P1  UNL     1      -7.430  -0.349   0.289  1.00  0.00           P  
HETATM   43  O8  UNL     1      -7.759   0.991  -0.376  1.00  0.00           O  
HETATM   44  O9  UNL     1      -7.881  -0.173   1.912  1.00  0.00           O  
HETATM   45  O10 UNL     1      -8.243  -1.581  -0.483  1.00  0.00           O  
HETATM   46  P2  UNL     1      -8.606  -2.893   0.493  1.00  0.00           P  
HETATM   47  O11 UNL     1      -7.905  -2.808   1.828  1.00  0.00           O  
HETATM   48  O12 UNL     1      -8.139  -4.316  -0.328  1.00  0.00           O  
HETATM   49  O13 UNL     1     -10.269  -2.992   0.758  1.00  0.00           O  
HETATM   50  C32 UNL     1     -10.827  -1.770   1.098  1.00  0.00           C  
HETATM   51  C33 UNL     1     -12.313  -1.868   1.346  1.00  0.00           C  
HETATM   52  O14 UNL     1     -12.863  -0.657   1.673  1.00  0.00           O  
HETATM   53  C34 UNL     1     -13.980  -0.423   0.908  1.00  0.00           C  
HETATM   54  N3  UNL     1     -14.222   0.997   0.764  1.00  0.00           N  
HETATM   55  C35 UNL     1     -13.427   2.031   1.061  1.00  0.00           C  
HETATM   56  N4  UNL     1     -14.038   3.195   0.769  1.00  0.00           N  
HETATM   57  C36 UNL     1     -15.259   2.906   0.271  1.00  0.00           C  
HETATM   58  C37 UNL     1     -16.298   3.714  -0.187  1.00  0.00           C  
HETATM   59  N5  UNL     1     -16.118   5.108  -0.159  1.00  0.00           N  
HETATM   60  N6  UNL     1     -17.416   3.118  -0.631  1.00  0.00           N  
HETATM   61  C38 UNL     1     -17.519   1.780  -0.631  1.00  0.00           C  
HETATM   62  N7  UNL     1     -16.517   1.002  -0.190  1.00  0.00           N  
HETATM   63  C39 UNL     1     -15.355   1.535   0.275  1.00  0.00           C  
HETATM   64  C40 UNL     1     -13.639  -1.101  -0.404  1.00  0.00           C  
HETATM   65  O15 UNL     1     -14.792  -1.383  -1.135  1.00  0.00           O  
HETATM   66  C41 UNL     1     -13.002  -2.398   0.123  1.00  0.00           C  
HETATM   67  O16 UNL     1     -14.052  -3.240   0.418  1.00  0.00           O  
HETATM   68  P3  UNL     1     -14.065  -4.687  -0.406  1.00  0.00           P  
HETATM   69  O17 UNL     1     -15.049  -5.662   0.246  1.00  0.00           O  
HETATM   70  O18 UNL     1     -14.628  -4.417  -1.976  1.00  0.00           O  
HETATM   71  O19 UNL     1     -12.535  -5.402  -0.537  1.00  0.00           O  
HETATM   72  H1  UNL     1      19.162  -0.327  -0.620  1.00  0.00           H  
HETATM   73  H2  UNL     1      18.677  -2.063  -0.624  1.00  0.00           H  
HETATM   74  H3  UNL     1      17.866  -0.812   0.476  1.00  0.00           H  
HETATM   75  H4  UNL     1      17.220  -1.430  -2.361  1.00  0.00           H  
HETATM   76  H5  UNL     1      17.522   0.332  -2.020  1.00  0.00           H  
HETATM   77  H6  UNL     1      15.885   0.096  -0.066  1.00  0.00           H  
HETATM   78  H7  UNL     1      15.699  -1.637  -0.520  1.00  0.00           H  
HETATM   79  H8  UNL     1      14.945  -0.971  -2.784  1.00  0.00           H  
HETATM   80  H9  UNL     1      15.152   0.766  -2.415  1.00  0.00           H  
HETATM   81  H10 UNL     1      13.394  -1.156  -0.822  1.00  0.00           H  
HETATM   82  H11 UNL     1      13.583   0.576  -0.461  1.00  0.00           H  
HETATM   83  H12 UNL     1      12.673   1.189  -2.708  1.00  0.00           H  
HETATM   84  H13 UNL     1      12.523  -1.639  -3.027  1.00  0.00           H  
HETATM   85  H14 UNL     1      11.370   1.263  -0.779  1.00  0.00           H  
HETATM   86  H15 UNL     1      10.323   0.690  -2.081  1.00  0.00           H  
HETATM   87  H16 UNL     1      10.525  -1.742  -1.218  1.00  0.00           H  
HETATM   88  H17 UNL     1      10.263  -1.820   3.641  1.00  0.00           H  
HETATM   89  H18 UNL     1      11.761  -2.607   2.994  1.00  0.00           H  
HETATM   90  H19 UNL     1      11.421   0.122   3.677  1.00  0.00           H  
HETATM   91  H20 UNL     1      12.798  -0.504   2.629  1.00  0.00           H  
HETATM   92  H21 UNL     1      11.822   0.953   1.134  1.00  0.00           H  
HETATM   93  H22 UNL     1      10.202   1.814   2.660  1.00  0.00           H  
HETATM   94  H23 UNL     1       9.310   0.265   2.702  1.00  0.00           H  
HETATM   95  H24 UNL     1       9.532   2.264   0.308  1.00  0.00           H  
HETATM   96  H25 UNL     1       7.346   1.661  -0.169  1.00  0.00           H  
HETATM   97  H26 UNL     1       6.527  -0.487   0.676  1.00  0.00           H  
HETATM   98  H27 UNL     1       7.568  -0.447   2.106  1.00  0.00           H  
HETATM   99  H28 UNL     1       6.231   1.513   2.967  1.00  0.00           H  
HETATM  100  H29 UNL     1       5.276   0.054   2.745  1.00  0.00           H  
HETATM  101  H30 UNL     1       4.019   1.888   1.940  1.00  0.00           H  
HETATM  102  H31 UNL     1       4.458   0.988   0.456  1.00  0.00           H  
HETATM  103  H32 UNL     1       3.322   3.860  -2.418  1.00  0.00           H  
HETATM  104  H33 UNL     1       3.438   2.215  -1.780  1.00  0.00           H  
HETATM  105  H34 UNL     1       2.043   4.632  -0.490  1.00  0.00           H  
HETATM  106  H35 UNL     1       1.271   3.337  -1.438  1.00  0.00           H  
HETATM  107  H36 UNL     1       1.771   3.326   1.394  1.00  0.00           H  
HETATM  108  H37 UNL     1       0.943   1.374   2.419  1.00  0.00           H  
HETATM  109  H38 UNL     1       2.329   0.287   2.097  1.00  0.00           H  
HETATM  110  H39 UNL     1       0.799  -1.209   0.702  1.00  0.00           H  
HETATM  111  H40 UNL     1       0.594  -1.163   2.444  1.00  0.00           H  
HETATM  112  H41 UNL     1      -1.588  -0.622   2.107  1.00  0.00           H  
HETATM  113  H42 UNL     1      -3.337   1.630   0.306  1.00  0.00           H  
HETATM  114  H43 UNL     1      -3.718  -1.010   1.331  1.00  0.00           H  
HETATM  115  H44 UNL     1      -3.715  -1.843  -2.156  1.00  0.00           H  
HETATM  116  H45 UNL     1      -4.010  -2.022  -0.407  1.00  0.00           H  
HETATM  117  H46 UNL     1      -2.312  -1.563  -0.995  1.00  0.00           H  
HETATM  118  H47 UNL     1      -2.855   1.811  -1.924  1.00  0.00           H  
HETATM  119  H48 UNL     1      -2.353   0.247  -2.630  1.00  0.00           H  
HETATM  120  H49 UNL     1      -3.959   0.896  -2.987  1.00  0.00           H  
HETATM  121  H50 UNL     1      -5.514   1.243  -0.869  1.00  0.00           H  
HETATM  122  H51 UNL     1      -5.713  -0.222  -1.844  1.00  0.00           H  
HETATM  123  H52 UNL     1      -7.089  -0.134   2.481  1.00  0.00           H  
HETATM  124  H53 UNL     1      -7.708  -4.098  -1.199  1.00  0.00           H  
HETATM  125  H54 UNL     1     -10.578  -0.986   0.359  1.00  0.00           H  
HETATM  126  H55 UNL     1     -10.290  -1.451   2.040  1.00  0.00           H  
HETATM  127  H56 UNL     1     -12.432  -2.533   2.228  1.00  0.00           H  
HETATM  128  H57 UNL     1     -14.844  -0.898   1.418  1.00  0.00           H  
HETATM  129  H58 UNL     1     -12.437   1.933   1.477  1.00  0.00           H  
HETATM  130  H59 UNL     1     -15.566   5.576   0.580  1.00  0.00           H  
HETATM  131  H60 UNL     1     -16.550   5.693  -0.899  1.00  0.00           H  
HETATM  132  H61 UNL     1     -18.448   1.370  -1.003  1.00  0.00           H  
HETATM  133  H62 UNL     1     -12.916  -0.494  -0.946  1.00  0.00           H  
HETATM  134  H63 UNL     1     -14.527  -1.666  -2.027  1.00  0.00           H  
HETATM  135  H64 UNL     1     -12.313  -2.746  -0.642  1.00  0.00           H  
HETATM  136  H65 UNL     1     -13.931  -4.421  -2.652  1.00  0.00           H  
HETATM  137  H66 UNL     1     -11.952  -4.754  -0.998  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    8   83
CONECT    7   84
CONECT    8    9   85   86
CONECT    9   10   10   87
CONECT   10   11   15
CONECT   11   12   12   13
CONECT   13   14   88   89
CONECT   14   15   90   91
CONECT   15   16   92
CONECT   16   17   93   94
CONECT   17   18   18   95
CONECT   18   19   96
CONECT   19   20   97   98
CONECT   20   21   99  100
CONECT   21   22  101  102
CONECT   22   23   23   24
CONECT   24   25
CONECT   25   26  103  104
CONECT   26   27  105  106
CONECT   27   28  107
CONECT   28   29   29   30
CONECT   30   31  108  109
CONECT   31   32  110  111
CONECT   32   33  112
CONECT   33   34   34   35
CONECT   35   36   37  113
CONECT   36  114
CONECT   37   38   39   40
CONECT   38  115  116  117
CONECT   39  118  119  120
CONECT   40   41  121  122
CONECT   41   42
CONECT   42   43   43   44   45
CONECT   44  123
CONECT   45   46
CONECT   46   47   47   48   49
CONECT   48  124
CONECT   49   50
CONECT   50   51  125  126
CONECT   51   52   66  127
CONECT   52   53
CONECT   53   54   64  128
CONECT   54   55   63
CONECT   55   56   56  129
CONECT   56   57
CONECT   57   58   58   63
CONECT   58   59   60
CONECT   59  130  131
CONECT   60   61   61
CONECT   61   62  132
CONECT   62   63   63
CONECT   64   65   66  133
CONECT   65  134
CONECT   66   67  135
CONECT   67   68
CONECT   68   69   69   70   71
CONECT   70  136
CONECT   71  137
END
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SMILES for HMDB0301546 ((5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA)

CCCCCC(O)CC=C1C(CC=CCCCC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2OP(O)(O)=O)N2C=NC3=C2N=CN=C3N)CCC1=O
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INCHI for HMDB0301546 ((5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA)

InChI=1S/C41H66N7O19P3S/c1-4-5-8-12-27(49)15-16-28-26(14-17-29(28)50)11-9-6-7-10-13-32(52)71-21-20-43-31(51)18-19-44-39(55)36(54)41(2,3)23-64-70(61,62)67-69(59,60)63-22-30-35(66-68(56,57)58)34(53)40(65-30)48-25-47-33-37(42)45-24-46-38(33)48/h6,9,16,24-27,30,34-36,40,49,53-54H,4-5,7-8,10-15,17-23H2,1-3H3,(H,43,51)(H,44,55)(H,59,60)(H,61,62)(H2,42,45,46)(H2,56,57,58)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
4-({[({[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-2-hydroxy-N-(2-{[2-({7-[2-(3-hydroxyoctylidene)-3-oxocyclopentyl]hept-5-enoyl}sulfanyl)ethyl]-C-hydroxycarbonimidoyl}ethyl)-3,3-dimethylbutanimidateGenerator
4-({[({[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-2-hydroxy-N-(2-{[2-({7-[2-(3-hydroxyoctylidene)-3-oxocyclopentyl]hept-5-enoyl}sulphanyl)ethyl]-C-hydroxycarbonimidoyl}ethyl)-3,3-dimethylbutanimidateGenerator
4-({[({[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-2-hydroxy-N-(2-{[2-({7-[2-(3-hydroxyoctylidene)-3-oxocyclopentyl]hept-5-enoyl}sulphanyl)ethyl]-C-hydroxycarbonimidoyl}ethyl)-3,3-dimethylbutanimidic acidGenerator
Chemical FormulaC41H66N7O19P3S
Average Molecular Weight1085.99
Monoisotopic Molecular Weight1085.334705101
IUPAC Name{[5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-({[hydroxy({[hydroxy({3-hydroxy-3-[(2-{[2-({7-[2-(3-hydroxyoctylidene)-3-oxocyclopentyl]hept-5-enoyl}sulfanyl)ethyl]carbamoyl}ethyl)carbamoyl]-2,2-dimethylpropoxy})phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-3-yl]oxy}phosphonic acid
Traditional Name[5-(6-aminopurin-9-yl)-4-hydroxy-2-({[hydroxy([hydroxy(3-hydroxy-3-[(2-{[2-({7-[2-(3-hydroxyoctylidene)-3-oxocyclopentyl]hept-5-enoyl}sulfanyl)ethyl]carbamoyl}ethyl)carbamoyl]-2,2-dimethylpropoxy)phosphoryl]oxy)phosphoryl]oxy}methyl)oxolan-3-yl]oxyphosphonic acid
CAS Registry NumberNot Available
SMILES
CCCCCC(O)CC=C1C(CC=CCCCC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC2OC(C(O)C2OP(O)(O)=O)N2C=NC3=C2N=CN=C3N)CCC1=O
InChI Identifier
InChI=1S/C41H66N7O19P3S/c1-4-5-8-12-27(49)15-16-28-26(14-17-29(28)50)11-9-6-7-10-13-32(52)71-21-20-43-31(51)18-19-44-39(55)36(54)41(2,3)23-64-70(61,62)67-69(59,60)63-22-30-35(66-68(56,57)58)34(53)40(65-30)48-25-47-33-37(42)45-24-46-38(33)48/h6,9,16,24-27,30,34-36,40,49,53-54H,4-5,7-8,10-15,17-23H2,1-3H3,(H,43,51)(H,44,55)(H,59,60)(H,61,62)(H2,42,45,46)(H2,56,57,58)
InChI KeyNYGXGWCQLFQCML-UHFFFAOYSA-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
logP1.84ALOGPS
logP-1.2ChemAxon
logS-2.9ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.01ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count19ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area400.93 ŲChemAxon
Rotatable Bond Count32ChemAxon
Refractivity257.47 m³·mol⁻¹ChemAxon
Polarizability108.03 ųChemAxon
Number of Rings4ChemAxon
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]+296.07332859911
AllCCS[M+H-H2O]+296.73532859911
AllCCS[M+Na]+295.22632859911
AllCCS[M+NH4]+295.4232859911
AllCCS[M-H]-299.54432859911
AllCCS[M+Na-2H]-305.46332859911
AllCCS[M+HCOO]-311.87432859911
DeepCCS[M+H]+286.33530932474
DeepCCS[M-H]-284.5230932474
DeepCCS[M-2H]-318.55130932474
DeepCCS[M+Na]+292.57330932474

Predicted Kovats Retention Indices

Not Available
Spectra

GC-MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
MSMass Spectrum (Electron Ionization)Not Available2022-08-06Not AvailableView Spectrum

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA 10V, Positive-QTOFsplash10-00kr-9000000000-1b40786762d1a2c28cf42021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA 20V, Positive-QTOFsplash10-0l0i-9400000003-ec764642e4f6bfcdb7b82021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA 40V, Positive-QTOFsplash10-004i-0000190000-4188e78ab489d637d8062021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA 10V, Negative-QTOFsplash10-001i-9000000000-2eb5cd7b8779bab9a43d2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA 20V, Negative-QTOFsplash10-00o0-9000101101-0e4bdbb2b3a41dc673872021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (5Z)-7-[(1R,2E)-2-[(3S)-3-hydroxyoctylidene]-3-oxocyclopentyl]hept-5-enoyl-CoA 40V, Negative-QTOFsplash10-00n0-9002301300-3343d0bf947bbbb4092b2021-10-21Wishart 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. Abe T, Fujino T, Fukuyama R, Minoshima S, Shimizu N, Toh H, Suzuki H, Yamamoto T: Human long-chain acyl-CoA synthetase: structure and chromosomal location. J Biochem. 1992 Jan;111(1):123-8. [PubMed:1607358 ]
  2. Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]