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Showing metabocard for (3R)-3-hydroxyoctanoyl-CoA (HMDB0301452)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-22 00:02:47 UTC
Update Date2021-10-01 16:54:36 UTC
HMDB IDHMDB0301452
Secondary Accession NumbersNone
Metabolite Identification
Common Name(3R)-3-hydroxyoctanoyl-CoA
Description(3r)-3-hydroxyoctanoyl-coa is an acyl-CoA or acyl-coenzyme A. More specifically, it is a (3R)-3-hydroxyoctanoic acid thioester of coenzyme A. (3r)-3-hydroxyoctanoyl-coa is an acyl-CoA with 3 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. (3r)-3-hydroxyoctanoyl-coa is therefore classified as a short 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. (3r)-3-hydroxyoctanoyl-coa, being a short chain acyl-CoA is a substrate for short 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, (3R)-3-hydroxyoctanoyl-CoA is transported into the mitochondria, the locus of beta oxidation. Transport of (3R)-3-hydroxyoctanoyl-CoA into the mitochondria requires carnitine palmitoyltransferase 1 (CPT1), which converts (3R)-3-hydroxyoctanoyl-CoA into (3R)-3-hydroxyoctanoylcarnitine, which gets transported into the mitochondrial matrix. Once in the matrix, (3R)-3-hydroxyoctanoylcarnitine is converted back to (3R)-3-hydroxyoctanoyl-CoA by CPT2, whereupon beta-oxidation can begin. Beta oxidation of (3R)-3-hydroxyoctanoyl-CoA occurs in four steps. First, since (3R)-3-hydroxyoctanoyl-CoA is a short chain acyl-CoA it is the substrate for a short chain acyl-CoA dehydrogenase, which catalyzes dehydrogenation of (3R)-3-hydroxyoctanoyl-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 (3R)-3-hydroxyoctanoyl-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 HMDB0301452 ((3R)-3-hydroxyoctanoyl-CoA)


  Mrv1652304102105012D          

 58 60  0  0  0  0            999 V2000
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M  END
Download

3D MOL for HMDB0301452 ((3R)-3-hydroxyoctanoyl-CoA)

HMDB0301452
     RDKit          3D
(3R)-3-hydroxyoctanoyl-CoA
108110  0  0  0  0  0  0  0  0999 V2000
    9.2737    1.5597   -3.8316 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3334    1.6878   -2.3120 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6469    1.1650   -1.7932 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8960   -0.2695   -2.0866 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9588   -1.2891   -1.5684 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8262   -1.3788   -0.0932 C   0  0  0  0  0  0  0  0  0  0  0  0
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    8.9713    2.5514   -4.2339 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4716    1.2098   -1.8638 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3090    2.7759   -2.0218 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4398    1.7445   -2.4172 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8389    1.5083   -0.7797 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.9200   -0.4041   -3.2186 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.9790   -0.5270   -1.7954 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2179   -2.3203   -1.9694 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9569   -1.0815   -2.0546 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3427   -2.4284    0.1345 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.9927   -2.0102    1.4089 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0131   -0.7028    1.7137 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3298    0.5997    0.5708 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0622   -3.9663   -0.7630 H   0  0  0  0  0  0  0  0  0  0  0  0
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    7.5187   -4.9773    0.9840 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9063   -3.4041    1.6676 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5823   -5.0494    2.2646 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2522   -3.9636    2.8549 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3574   -3.6531    4.2979 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3953   -2.1132    4.2914 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9521   -1.2850    4.1090 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8518   -1.8277    1.4650 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0058    1.4358    1.1695 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2799   -1.2110    0.2080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6076   -1.2302    1.0128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3147   -1.0106    2.7453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8018   -0.2778    1.9059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8271    2.5881    2.3379 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8943    2.3614    2.7112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3951    1.3386    3.5501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7268    1.5038    0.4529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2007    2.2582   -0.0449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9303   -0.7373   -1.9086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8168    1.4656   -3.9351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4000    2.2894   -2.0237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9378    3.9326   -1.5254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4064    3.2299    0.8982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6269    1.3808    2.1650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3780   -1.0442    2.7479 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7040   -4.4159    0.9416 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1846   -4.9099    0.1689 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7170   -0.4967   -2.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9633    1.9356    0.4399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4191    3.1691    2.4483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4639    4.0740   -0.1536 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1427    2.7092   -2.1038 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1243    5.1733   -1.0610 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
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  9 10  2  0
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 42100  1  0
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 46102  1  0
 48103  1  0
 51104  1  0
 52105  1  0
 53106  1  0
 57107  1  0
 58108  1  0
M  END
Download

3D SDF for HMDB0301452 ((3R)-3-hydroxyoctanoyl-CoA)


  Mrv1652304102105012D          

 58 60  0  0  0  0            999 V2000
   14.1781   -7.9457    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.1781   -7.1207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.4637   -6.7082    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   12.7492   -7.1207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0347   -6.7082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3202   -7.1207    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   10.6058   -6.7082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6058   -5.8832    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.8913   -7.1207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1768   -6.7082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.4624   -7.1207    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.7479   -6.7082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7479   -5.8832    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0334   -7.1207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0334   -7.9457    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.3190   -6.7082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9065   -7.4227    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.7315   -5.9937    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.6045   -6.2957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8900   -6.7082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.1755   -6.2957    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.7630   -7.0102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5880   -5.5812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4611   -5.8832    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7466   -6.2957    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    3.1591   -7.0102    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.3341   -5.5812    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0321   -6.7082    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3177   -6.2957    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.6032   -6.7082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5169   -7.5287    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2900   -7.7002    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6256   -8.4539    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2131   -9.1684    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7651   -9.7815    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5188   -9.4459    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.2725   -9.7815    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9399   -9.2965    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8537   -8.4761    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1000   -8.1405    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4326   -8.6254    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3587  -10.6019    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7025   -6.9857    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.5230   -6.8995    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1505   -6.3727    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3220   -5.5657    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.2911   -5.0136    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.8431   -5.6267    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2610   -4.4006    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9042   -4.4616    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.8926   -6.7082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6071   -7.1207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6071   -7.9457    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3215   -6.7082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0360   -7.1207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7505   -6.7082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.4650   -7.1207    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.1794   -6.7082    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 12 13  2  0  0  0  0
 12 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  1  0  0  0  0
 16 17  1  0  0  0  0
 16 18  1  0  0  0  0
 16 19  1  0  0  0  0
 19 20  1  0  0  0  0
 20 21  1  0  0  0  0
 21 22  2  0  0  0  0
 21 23  1  0  0  0  0
 21 24  1  0  0  0  0
 24 25  1  0  0  0  0
 25 26  2  0  0  0  0
 25 27  1  0  0  0  0
 25 28  1  0  0  0  0
 28 29  1  0  0  0  0
 29 30  1  0  0  0  0
 30 31  1  0  0  0  0
 31 32  1  0  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 34 35  2  0  0  0  0
 35 36  1  0  0  0  0
 36 37  1  0  0  0  0
 37 38  2  0  0  0  0
 38 39  1  0  0  0  0
 39 40  2  0  0  0  0
 40 41  1  0  0  0  0
 36 41  2  0  0  0  0
 33 41  1  0  0  0  0
 37 42  1  0  0  0  0
 32 43  1  0  0  0  0
 43 44  1  0  0  0  0
 43 45  1  0  0  0  0
 30 45  1  0  0  0  0
 45 46  1  0  0  0  0
 46 47  1  0  0  0  0
 47 48  2  0  0  0  0
 47 49  1  0  0  0  0
 47 50  1  0  0  0  0
  2 51  1  0  0  0  0
 51 52  1  0  0  0  0
 52 53  1  0  0  0  0
 52 54  1  0  0  0  0
 54 55  1  0  0  0  0
 55 56  1  0  0  0  0
 56 57  1  0  0  0  0
 57 58  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0301452

> <DATABASE_NAME>
hmdb

> <SMILES>
CCCCCC(O)CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N

> <INCHI_IDENTIFIER>
InChI=1S/C29H50N7O18P3S/c1-4-5-6-7-17(37)12-20(39)58-11-10-31-19(38)8-9-32-27(42)24(41)29(2,3)14-51-57(48,49)54-56(46,47)50-13-18-23(53-55(43,44)45)22(40)28(52-18)36-16-35-21-25(30)33-15-34-26(21)36/h15-18,22-24,28,37,40-41H,4-14H2,1-3H3,(H,31,38)(H,32,42)(H,46,47)(H,48,49)(H2,30,33,34)(H2,43,44,45)

> <INCHI_KEY>
ATVGTMKWKDUCMS-UHFFFAOYSA-N

> <FORMULA>
C29H50N7O18P3S

> <MOLECULAR_WEIGHT>
909.73

> <EXACT_MASS>
909.214589966

> <JCHEM_ACCEPTOR_COUNT>
18

> <JCHEM_ATOM_COUNT>
108

> <JCHEM_AVERAGE_POLARIZABILITY>
84.59909418142098

> <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-[(3-hydroxyoctanoyl)sulfanyl]ethyl}carbamoyl)ethyl]carbamoyl}-2,2-dimethylpropoxy)phosphoryl]oxy})phosphoryl]oxy}methyl)oxolan-3-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-0.03

> <JCHEM_LOGP>
-4.189051008147961

> <ALOGPS_LOGS>
-2.42

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.900120734776186

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.820978781339821

> <JCHEM_PKA_STRONGEST_BASIC>
4.006053268556904

> <JCHEM_POLAR_SURFACE_AREA>
383.86

> <JCHEM_REFRACTIVITY>
201.35540000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
26

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.44e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[5-(6-aminopurin-9-yl)-4-hydroxy-2-({[hydroxy([hydroxy(3-hydroxy-3-{[2-({2-[(3-hydroxyoctanoyl)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 HMDB0301452 ((3R)-3-hydroxyoctanoyl-CoA)

HMDB0301452
     RDKit          3D
(3R)-3-hydroxyoctanoyl-CoA
108110  0  0  0  0  0  0  0  0999 V2000
    9.2737    1.5597   -3.8316 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3334    1.6878   -2.3120 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6469    1.1650   -1.7932 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.8960   -0.2695   -2.0866 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9588   -1.2891   -1.5684 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8262   -1.3788   -0.0932 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0813   -1.5884    0.5326 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9283   -0.4421    0.5826 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.5074   -0.4219    0.2234 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.9938    0.7523    0.3327 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.4121   -1.6518   -0.3017 S   0  0  0  0  0  0  0  0  0  0  0  0
    6.8986   -3.3370   -0.2104 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.0695   -3.9503    1.1387 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.9275   -4.0647    1.9653 N   0  0  0  0  0  0  0  0  0  0  0  0
    5.1452   -3.0122    2.4529 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.3881   -1.8171    2.1885 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.9558   -3.2535    3.3343 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.2479   -1.9864    3.6145 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.7199   -1.3780    2.4021 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.0201   -0.1615    2.5077 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8783    0.3762    3.6274 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.4621    0.4498    1.2582 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6832   -0.3207    0.1388 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0024    0.7748    1.5046 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7219   -0.5178    1.8593 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0762    1.7968    2.5971 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6644    1.2910    0.2596 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6302    0.3622   -0.7779 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3883    0.8947   -2.1660 P   0  0  0  0  0  5  0  0  0  0  0  0
   -0.4114    0.9822   -3.3158 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.6372   -0.1487   -2.6466 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9954    2.4495   -1.8964 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.6435    2.5516   -2.3353 P   0  0  0  0  0  5  0  0  0  0  0  0
   -3.8503    3.9527   -2.8909 O   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8986    1.4591   -3.5759 O   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6460    2.3556   -1.0307 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9254    2.8741   -1.2044 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.7812    2.6589    0.0278 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.8981    1.2882    0.3061 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.0167    1.1563    1.1262 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.5374   -0.1715    1.1466 N   0  0  0  0  0  0  0  0  0  0  0  0
   -8.1492   -1.1770    1.9854 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8483   -2.2859    1.7133 N   0  0  0  0  0  0  0  0  0  0  0  0
   -9.7105   -2.0327    0.6905 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.6416   -2.7934    0.0241 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.8321   -4.1512    0.3939 N   0  0  0  0  0  0  0  0  0  0  0  0
  -11.3365   -2.1980   -0.9665 N   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1099   -0.8960   -1.2778 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.2076   -0.1490   -0.6362 N   0  0  0  0  0  0  0  0  0  0  0  0
   -9.4903   -0.6971    0.3581 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.9718    2.2386    0.7657 C   0  0  0  0  0  0  0  0  0  0  0  0
   -9.1894    3.1152    1.8583 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.2127    3.0232   -0.2876 C   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4971    2.5621   -1.5704 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2011    3.7768   -2.4977 P   0  0  0  0  0  5  0  0  0  0  0  0
   -8.4078    3.9645   -3.7600 O   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7956    3.2972   -2.8290 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.2633    5.1830   -1.5775 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.5197    0.7959   -4.0985 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2808    1.3167   -4.1949 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9713    2.5514   -4.2339 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.4716    1.2098   -1.8638 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3090    2.7759   -2.0218 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.4398    1.7445   -2.4172 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.8389    1.5083   -0.7797 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.9200   -0.4041   -3.2186 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.9790   -0.5270   -1.7954 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.2179   -2.3203   -1.9694 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.9569   -1.0815   -2.0546 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3427   -2.4284    0.1345 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.9927   -2.0102    1.4089 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.0131   -0.7028    1.7137 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3298    0.5997    0.5708 H   0  0  0  0  0  0  0  0  0  0  0  0
    6.0622   -3.9663   -0.7630 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.7776   -3.5527   -0.8830 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.5187   -4.9773    0.9840 H   0  0  0  0  0  0  0  0  0  0  0  0
    7.9063   -3.4041    1.6676 H   0  0  0  0  0  0  0  0  0  0  0  0
    5.5823   -5.0494    2.2646 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2522   -3.9636    2.8549 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.3574   -3.6531    4.2979 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.3953   -2.1132    4.2914 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.9521   -1.2850    4.1090 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8518   -1.8277    1.4650 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.0058    1.4358    1.1695 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.2799   -1.2110    0.2080 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6076   -1.2302    1.0128 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3147   -1.0106    2.7453 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8018   -0.2778    1.9059 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8271    2.5881    2.3379 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.8943    2.3614    2.7112 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3951    1.3386    3.5501 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7268    1.5038    0.4529 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2007    2.2582   -0.0449 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9303   -0.7373   -1.9086 H   0  0  0  0  0  0  0  0  0  0  0  0
   -4.8168    1.4656   -3.9351 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4000    2.2894   -2.0237 H   0  0  0  0  0  0  0  0  0  0  0  0
   -5.9378    3.9326   -1.5254 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4064    3.2299    0.8982 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6269    1.3808    2.1650 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3780   -1.0442    2.7479 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7040   -4.4159    0.9416 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1846   -4.9099    0.1689 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7170   -0.4967   -2.0922 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.9633    1.9356    0.4399 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4191    3.1691    2.4483 H   0  0  0  0  0  0  0  0  0  0  0  0
   -8.4639    4.0740   -0.1536 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.1427    2.7092   -2.1038 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1243    5.1733   -1.0610 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
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  9 10  2  0
  9 11  1  0
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 58108  1  0
M  END
Download

PDB for HMDB0301452 ((3R)-3-hydroxyoctanoyl-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      26.466 -14.832   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      26.466 -13.292   0.000  0.00  0.00           C+0
HETATM    3  S   UNK     0      25.132 -12.522   0.000  0.00  0.00           S+0
HETATM    4  C   UNK     0      23.798 -13.292   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      22.465 -12.522   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      21.131 -13.292   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      19.797 -12.522   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      19.797 -10.982   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0      18.464 -13.292   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      17.130 -12.522   0.000  0.00  0.00           C+0
HETATM   11  N   UNK     0      15.796 -13.292   0.000  0.00  0.00           N+0
HETATM   12  C   UNK     0      14.463 -12.522   0.000  0.00  0.00           C+0
HETATM   13  O   UNK     0      14.463 -10.982   0.000  0.00  0.00           O+0
HETATM   14  C   UNK     0      13.129 -13.292   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      13.129 -14.832   0.000  0.00  0.00           O+0
HETATM   16  C   UNK     0      11.795 -12.522   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      11.025 -13.856   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      12.565 -11.188   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      10.462 -11.752   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0       9.128 -12.522   0.000  0.00  0.00           O+0
HETATM   21  P   UNK     0       7.794 -11.752   0.000  0.00  0.00           P+0
HETATM   22  O   UNK     0       7.024 -13.086   0.000  0.00  0.00           O+0
HETATM   23  O   UNK     0       8.564 -10.418   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0       6.461 -10.982   0.000  0.00  0.00           O+0
HETATM   25  P   UNK     0       5.127 -11.752   0.000  0.00  0.00           P+0
HETATM   26  O   UNK     0       5.897 -13.086   0.000  0.00  0.00           O+0
HETATM   27  O   UNK     0       4.357 -10.418   0.000  0.00  0.00           O+0
HETATM   28  O   UNK     0       3.793 -12.522   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0       2.460 -11.752   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0       1.126 -12.522   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0       0.965 -14.054   0.000  0.00  0.00           O+0
HETATM   32  C   UNK     0      -0.541 -14.374   0.000  0.00  0.00           C+0
HETATM   33  N   UNK     0      -1.168 -15.781   0.000  0.00  0.00           N+0
HETATM   34  C   UNK     0      -0.398 -17.114   0.000  0.00  0.00           C+0
HETATM   35  N   UNK     0      -1.428 -18.259   0.000  0.00  0.00           N+0
HETATM   36  C   UNK     0      -2.835 -17.632   0.000  0.00  0.00           C+0
HETATM   37  C   UNK     0      -4.242 -18.259   0.000  0.00  0.00           C+0
HETATM   38  N   UNK     0      -5.488 -17.354   0.000  0.00  0.00           N+0
HETATM   39  C   UNK     0      -5.327 -15.822   0.000  0.00  0.00           C+0
HETATM   40  N   UNK     0      -3.920 -15.196   0.000  0.00  0.00           N+0
HETATM   41  C   UNK     0      -2.674 -16.101   0.000  0.00  0.00           C+0
HETATM   42  N   UNK     0      -4.403 -19.790   0.000  0.00  0.00           N+0
HETATM   43  C   UNK     0      -1.311 -13.040   0.000  0.00  0.00           C+0
HETATM   44  O   UNK     0      -2.843 -12.879   0.000  0.00  0.00           O+0
HETATM   45  C   UNK     0      -0.281 -11.896   0.000  0.00  0.00           C+0
HETATM   46  O   UNK     0      -0.601 -10.389   0.000  0.00  0.00           O+0
HETATM   47  P   UNK     0       0.543  -9.359   0.000  0.00  0.00           P+0
HETATM   48  O   UNK     0       1.574 -10.503   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      -0.487  -8.214   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0       1.688  -8.328   0.000  0.00  0.00           O+0
HETATM   51  C   UNK     0      27.800 -12.522   0.000  0.00  0.00           C+0
HETATM   52  C   UNK     0      29.133 -13.292   0.000  0.00  0.00           C+0
HETATM   53  O   UNK     0      29.133 -14.832   0.000  0.00  0.00           O+0
HETATM   54  C   UNK     0      30.467 -12.522   0.000  0.00  0.00           C+0
HETATM   55  C   UNK     0      31.801 -13.292   0.000  0.00  0.00           C+0
HETATM   56  C   UNK     0      33.134 -12.522   0.000  0.00  0.00           C+0
HETATM   57  C   UNK     0      34.468 -13.292   0.000  0.00  0.00           C+0
HETATM   58  C   UNK     0      35.802 -12.522   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   54                                                  
CONECT   53   52                                                            
CONECT   54   52   55                                                       
CONECT   55   54   56                                                       
CONECT   56   55   57                                                       
CONECT   57   56   58                                                       
CONECT   58   57                                                            
MASTER        0    0    0    0    0    0    0    0   58    0  120    0
END
Download

3D PDB for HMDB0301452 ((3R)-3-hydroxyoctanoyl-CoA)

COMPND    HMDB0301452
HETATM    1  C1  UNL     1       9.274   1.560  -3.832  1.00  0.00           C  
HETATM    2  C2  UNL     1       9.333   1.688  -2.312  1.00  0.00           C  
HETATM    3  C3  UNL     1      10.647   1.165  -1.793  1.00  0.00           C  
HETATM    4  C4  UNL     1      10.896  -0.270  -2.087  1.00  0.00           C  
HETATM    5  C5  UNL     1       9.959  -1.289  -1.568  1.00  0.00           C  
HETATM    6  C6  UNL     1       9.826  -1.379  -0.093  1.00  0.00           C  
HETATM    7  O1  UNL     1      11.081  -1.588   0.533  1.00  0.00           O  
HETATM    8  C7  UNL     1       8.928  -0.442   0.583  1.00  0.00           C  
HETATM    9  C8  UNL     1       7.507  -0.422   0.223  1.00  0.00           C  
HETATM   10  O2  UNL     1       6.994   0.752   0.333  1.00  0.00           O  
HETATM   11  S1  UNL     1       6.412  -1.652  -0.302  1.00  0.00           S  
HETATM   12  C9  UNL     1       6.899  -3.337  -0.210  1.00  0.00           C  
HETATM   13  C10 UNL     1       7.070  -3.950   1.139  1.00  0.00           C  
HETATM   14  N1  UNL     1       5.928  -4.065   1.965  1.00  0.00           N  
HETATM   15  C11 UNL     1       5.145  -3.012   2.453  1.00  0.00           C  
HETATM   16  O3  UNL     1       5.388  -1.817   2.189  1.00  0.00           O  
HETATM   17  C12 UNL     1       3.956  -3.253   3.334  1.00  0.00           C  
HETATM   18  C13 UNL     1       3.248  -1.986   3.614  1.00  0.00           C  
HETATM   19  N2  UNL     1       2.720  -1.378   2.402  1.00  0.00           N  
HETATM   20  C14 UNL     1       2.020  -0.162   2.508  1.00  0.00           C  
HETATM   21  O4  UNL     1       1.878   0.376   3.627  1.00  0.00           O  
HETATM   22  C15 UNL     1       1.462   0.450   1.258  1.00  0.00           C  
HETATM   23  O5  UNL     1       1.683  -0.321   0.139  1.00  0.00           O  
HETATM   24  C16 UNL     1       0.002   0.775   1.505  1.00  0.00           C  
HETATM   25  C17 UNL     1      -0.722  -0.518   1.859  1.00  0.00           C  
HETATM   26  C18 UNL     1      -0.076   1.797   2.597  1.00  0.00           C  
HETATM   27  C19 UNL     1      -0.664   1.291   0.260  1.00  0.00           C  
HETATM   28  O6  UNL     1      -0.630   0.362  -0.778  1.00  0.00           O  
HETATM   29  P1  UNL     1      -1.388   0.895  -2.166  1.00  0.00           P  
HETATM   30  O7  UNL     1      -0.411   0.982  -3.316  1.00  0.00           O  
HETATM   31  O8  UNL     1      -2.637  -0.149  -2.647  1.00  0.00           O  
HETATM   32  O9  UNL     1      -1.995   2.450  -1.896  1.00  0.00           O  
HETATM   33  P2  UNL     1      -3.643   2.552  -2.335  1.00  0.00           P  
HETATM   34  O10 UNL     1      -3.850   3.953  -2.891  1.00  0.00           O  
HETATM   35  O11 UNL     1      -3.899   1.459  -3.576  1.00  0.00           O  
HETATM   36  O12 UNL     1      -4.646   2.356  -1.031  1.00  0.00           O  
HETATM   37  C20 UNL     1      -5.925   2.874  -1.204  1.00  0.00           C  
HETATM   38  C21 UNL     1      -6.781   2.659   0.028  1.00  0.00           C  
HETATM   39  O13 UNL     1      -6.898   1.288   0.306  1.00  0.00           O  
HETATM   40  C22 UNL     1      -8.017   1.156   1.126  1.00  0.00           C  
HETATM   41  N3  UNL     1      -8.537  -0.171   1.147  1.00  0.00           N  
HETATM   42  C23 UNL     1      -8.149  -1.177   1.985  1.00  0.00           C  
HETATM   43  N4  UNL     1      -8.848  -2.286   1.713  1.00  0.00           N  
HETATM   44  C24 UNL     1      -9.711  -2.033   0.691  1.00  0.00           C  
HETATM   45  C25 UNL     1     -10.642  -2.793   0.024  1.00  0.00           C  
HETATM   46  N5  UNL     1     -10.832  -4.151   0.394  1.00  0.00           N  
HETATM   47  N6  UNL     1     -11.337  -2.198  -0.966  1.00  0.00           N  
HETATM   48  C26 UNL     1     -11.110  -0.896  -1.278  1.00  0.00           C  
HETATM   49  N7  UNL     1     -10.208  -0.149  -0.636  1.00  0.00           N  
HETATM   50  C27 UNL     1      -9.490  -0.697   0.358  1.00  0.00           C  
HETATM   51  C28 UNL     1      -8.972   2.239   0.766  1.00  0.00           C  
HETATM   52  O14 UNL     1      -9.189   3.115   1.858  1.00  0.00           O  
HETATM   53  C29 UNL     1      -8.213   3.023  -0.288  1.00  0.00           C  
HETATM   54  O15 UNL     1      -8.497   2.562  -1.570  1.00  0.00           O  
HETATM   55  P3  UNL     1      -9.201   3.777  -2.498  1.00  0.00           P  
HETATM   56  O16 UNL     1      -8.408   3.965  -3.760  1.00  0.00           O  
HETATM   57  O17 UNL     1     -10.796   3.297  -2.829  1.00  0.00           O  
HETATM   58  O18 UNL     1      -9.263   5.183  -1.578  1.00  0.00           O  
HETATM   59  H1  UNL     1       8.520   0.796  -4.098  1.00  0.00           H  
HETATM   60  H2  UNL     1      10.281   1.317  -4.195  1.00  0.00           H  
HETATM   61  H3  UNL     1       8.971   2.551  -4.234  1.00  0.00           H  
HETATM   62  H4  UNL     1       8.472   1.210  -1.864  1.00  0.00           H  
HETATM   63  H5  UNL     1       9.309   2.776  -2.022  1.00  0.00           H  
HETATM   64  H6  UNL     1      11.440   1.744  -2.417  1.00  0.00           H  
HETATM   65  H7  UNL     1      10.839   1.508  -0.780  1.00  0.00           H  
HETATM   66  H8  UNL     1      10.920  -0.404  -3.219  1.00  0.00           H  
HETATM   67  H9  UNL     1      11.979  -0.527  -1.795  1.00  0.00           H  
HETATM   68  H10 UNL     1      10.218  -2.320  -1.969  1.00  0.00           H  
HETATM   69  H11 UNL     1       8.957  -1.082  -2.055  1.00  0.00           H  
HETATM   70  H12 UNL     1       9.343  -2.428   0.134  1.00  0.00           H  
HETATM   71  H13 UNL     1      10.993  -2.010   1.409  1.00  0.00           H  
HETATM   72  H14 UNL     1       9.013  -0.703   1.714  1.00  0.00           H  
HETATM   73  H15 UNL     1       9.330   0.600   0.571  1.00  0.00           H  
HETATM   74  H16 UNL     1       6.062  -3.966  -0.763  1.00  0.00           H  
HETATM   75  H17 UNL     1       7.778  -3.553  -0.883  1.00  0.00           H  
HETATM   76  H18 UNL     1       7.519  -4.977   0.984  1.00  0.00           H  
HETATM   77  H19 UNL     1       7.906  -3.404   1.668  1.00  0.00           H  
HETATM   78  H20 UNL     1       5.582  -5.049   2.265  1.00  0.00           H  
HETATM   79  H21 UNL     1       3.252  -3.964   2.855  1.00  0.00           H  
HETATM   80  H22 UNL     1       4.357  -3.653   4.298  1.00  0.00           H  
HETATM   81  H23 UNL     1       2.395  -2.113   4.291  1.00  0.00           H  
HETATM   82  H24 UNL     1       3.952  -1.285   4.109  1.00  0.00           H  
HETATM   83  H25 UNL     1       2.852  -1.828   1.465  1.00  0.00           H  
HETATM   84  H26 UNL     1       2.006   1.436   1.169  1.00  0.00           H  
HETATM   85  H27 UNL     1       1.280  -1.211   0.208  1.00  0.00           H  
HETATM   86  H28 UNL     1      -0.608  -1.230   1.013  1.00  0.00           H  
HETATM   87  H29 UNL     1      -0.315  -1.011   2.745  1.00  0.00           H  
HETATM   88  H30 UNL     1      -1.802  -0.278   1.906  1.00  0.00           H  
HETATM   89  H31 UNL     1      -0.827   2.588   2.338  1.00  0.00           H  
HETATM   90  H32 UNL     1       0.894   2.361   2.711  1.00  0.00           H  
HETATM   91  H33 UNL     1      -0.395   1.339   3.550  1.00  0.00           H  
HETATM   92  H34 UNL     1      -1.727   1.504   0.453  1.00  0.00           H  
HETATM   93  H35 UNL     1      -0.201   2.258  -0.045  1.00  0.00           H  
HETATM   94  H36 UNL     1      -2.930  -0.737  -1.909  1.00  0.00           H  
HETATM   95  H37 UNL     1      -4.817   1.466  -3.935  1.00  0.00           H  
HETATM   96  H38 UNL     1      -6.400   2.289  -2.024  1.00  0.00           H  
HETATM   97  H39 UNL     1      -5.938   3.933  -1.525  1.00  0.00           H  
HETATM   98  H40 UNL     1      -6.406   3.230   0.898  1.00  0.00           H  
HETATM   99  H41 UNL     1      -7.627   1.381   2.165  1.00  0.00           H  
HETATM  100  H42 UNL     1      -7.378  -1.044   2.748  1.00  0.00           H  
HETATM  101  H43 UNL     1     -11.704  -4.416   0.942  1.00  0.00           H  
HETATM  102  H44 UNL     1     -10.185  -4.910   0.169  1.00  0.00           H  
HETATM  103  H45 UNL     1     -11.717  -0.497  -2.092  1.00  0.00           H  
HETATM  104  H46 UNL     1      -9.963   1.936   0.440  1.00  0.00           H  
HETATM  105  H47 UNL     1      -8.419   3.169   2.448  1.00  0.00           H  
HETATM  106  H48 UNL     1      -8.464   4.074  -0.154  1.00  0.00           H  
HETATM  107  H49 UNL     1     -11.143   2.709  -2.104  1.00  0.00           H  
HETATM  108  H50 UNL     1     -10.124   5.173  -1.061  1.00  0.00           H  
CONECT    1    2   59   60   61
CONECT    2    3   62   63
CONECT    3    4   64   65
CONECT    4    5   66   67
CONECT    5    6   68   69
CONECT    6    7    8   70
CONECT    7   71
CONECT    8    9   72   73
CONECT    9   10   10   11
CONECT   11   12
CONECT   12   13   74   75
CONECT   13   14   76   77
CONECT   14   15   78
CONECT   15   16   16   17
CONECT   17   18   79   80
CONECT   18   19   81   82
CONECT   19   20   83
CONECT   20   21   21   22
CONECT   22   23   24   84
CONECT   23   85
CONECT   24   25   26   27
CONECT   25   86   87   88
CONECT   26   89   90   91
CONECT   27   28   92   93
CONECT   28   29
CONECT   29   30   30   31   32
CONECT   31   94
CONECT   32   33
CONECT   33   34   34   35   36
CONECT   35   95
CONECT   36   37
CONECT   37   38   96   97
CONECT   38   39   53   98
CONECT   39   40
CONECT   40   41   51   99
CONECT   41   42   50
CONECT   42   43   43  100
CONECT   43   44
CONECT   44   45   45   50
CONECT   45   46   47
CONECT   46  101  102
CONECT   47   48   48
CONECT   48   49  103
CONECT   49   50   50
CONECT   51   52   53  104
CONECT   52  105
CONECT   53   54  106
CONECT   54   55
CONECT   55   56   56   57   58
CONECT   57  107
CONECT   58  108
END
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SMILES for HMDB0301452 ((3R)-3-hydroxyoctanoyl-CoA)

CCCCCC(O)CC(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N
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INCHI for HMDB0301452 ((3R)-3-hydroxyoctanoyl-CoA)

InChI=1S/C29H50N7O18P3S/c1-4-5-6-7-17(37)12-20(39)58-11-10-31-19(38)8-9-32-27(42)24(41)29(2,3)14-51-57(48,49)54-56(46,47)50-13-18-23(53-55(43,44)45)22(40)28(52-18)36-16-35-21-25(30)33-15-34-26(21)36/h15-18,22-24,28,37,40-41H,4-14H2,1-3H3,(H,31,38)(H,32,42)(H,46,47)(H,48,49)(H2,30,33,34)(H2,43,44,45)
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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-[(3-hydroxyoctanoyl)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-[(3-hydroxyoctanoyl)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-[(3-hydroxyoctanoyl)sulphanyl]ethyl}-C-hydroxycarbonimidoyl)ethyl]-3,3-dimethylbutanimidic acidGenerator
Chemical FormulaC29H50N7O18P3S
Average Molecular Weight909.73
Monoisotopic Molecular Weight909.214589966
IUPAC Name{[5-(6-amino-9H-purin-9-yl)-4-hydroxy-2-({[hydroxy({[hydroxy(3-hydroxy-3-{[2-({2-[(3-hydroxyoctanoyl)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-[(3-hydroxyoctanoyl)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(=O)SCCNC(=O)CCNC(=O)C(O)C(C)(C)COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N
InChI Identifier
InChI=1S/C29H50N7O18P3S/c1-4-5-6-7-17(37)12-20(39)58-11-10-31-19(38)8-9-32-27(42)24(41)29(2,3)14-51-57(48,49)54-56(46,47)50-13-18-23(53-55(43,44)45)22(40)28(52-18)36-16-35-21-25(30)33-15-34-26(21)36/h15-18,22-24,28,37,40-41H,4-14H2,1-3H3,(H,31,38)(H,32,42)(H,46,47)(H,48,49)(H2,30,33,34)(H2,43,44,45)
InChI KeyATVGTMKWKDUCMS-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as 3-hydroxyacyl coas. These are organic compounds containing a 3-hydroxyl acylated coenzyme A derivative.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acyl thioesters
Direct Parent3-hydroxyacyl CoAs
Alternative Parents
Substituents
  • Coenzyme a or derivatives
  • Purine ribonucleoside 3',5'-bisphosphate
  • Purine ribonucleoside bisphosphate
  • Purine ribonucleoside diphosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Ribonucleoside 3'-phosphate
  • Beta amino acid or derivatives
  • Glycosyl compound
  • N-glycosyl compound
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • 6-aminopurine
  • Imidazopyrimidine
  • Purine
  • Monoalkyl phosphate
  • Aminopyrimidine
  • Fatty amide
  • Imidolactam
  • Monosaccharide
  • N-acyl-amine
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Alkyl phosphate
  • Phosphoric acid ester
  • Primary aromatic amine
  • Pyrimidine
  • Oxolane
  • Azole
  • Imidazole
  • Heteroaromatic compound
  • Amino acid or derivatives
  • Thiocarboxylic acid ester
  • Carboxamide group
  • Carbothioic s-ester
  • Secondary alcohol
  • Secondary carboxylic acid amide
  • Sulfenyl compound
  • Organoheterocyclic compound
  • Azacycle
  • Oxacycle
  • Thiocarboxylic acid or derivatives
  • Carboxylic acid derivative
  • Hydrocarbon derivative
  • Alcohol
  • Organic nitrogen compound
  • Amine
  • Organonitrogen compound
  • Carbonyl group
  • Organooxygen compound
  • Organosulfur compound
  • Organic oxygen compound
  • Organopnictogen compound
  • Primary amine
  • Organic oxide
  • Aromatic heteropolycyclic compound
Molecular FrameworkAromatic heteropolycyclic compounds
External DescriptorsNot Available
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
logP-0.03ALOGPS
logP-4.2ChemAxon
logS-2.4ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.01ChemAxon
Physiological Charge-4ChemAxon
Hydrogen Acceptor Count18ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area383.86 ŲChemAxon
Rotatable Bond Count26ChemAxon
Refractivity201.36 m³·mol⁻¹ChemAxon
Polarizability84.6 ųChemAxon
Number of Rings3ChemAxon
BioavailabilityNoChemAxon
Rule of FiveNoChemAxon
Ghose FilterNoChemAxon
Veber's RuleNoChemAxon
MDDR-like RuleYesChemAxon
Predicted Chromatographic Properties

Predicted Collision Cross Sections

PredictorAdduct TypeCCS Value (Å2)Reference
AllCCS[M+H]+269.3332859911
AllCCS[M+H-H2O]+269.90432859911
AllCCS[M+Na]+268.57432859911
AllCCS[M+NH4]+268.74932859911
AllCCS[M-H]-270.34532859911
AllCCS[M+Na-2H]-275.21432859911
AllCCS[M+HCOO]-280.5832859911
DeepCCS[M+H]+243.29630932474
DeepCCS[M-H]-241.47230932474
DeepCCS[M-2H]-274.90730932474
DeepCCS[M+Na]+250.03730932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3R)-3-hydroxyoctanoyl-CoA 10V, Negative-QTOFsplash10-0a4i-0000000029-abe85eb381168be13ad52021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3R)-3-hydroxyoctanoyl-CoA 20V, Negative-QTOFsplash10-0axu-6300201594-438242810146d0f49ec42021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3R)-3-hydroxyoctanoyl-CoA 40V, Negative-QTOFsplash10-0ar9-7602601921-d79c6670a43804328b1a2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3R)-3-hydroxyoctanoyl-CoA 10V, Positive-QTOFsplash10-01ox-0000000096-2dfa313df34cca5bbc522021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3R)-3-hydroxyoctanoyl-CoA 20V, Positive-QTOFsplash10-01p9-1500000291-15755dcc300e02901fc82021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - (3R)-3-hydroxyoctanoyl-CoA 40V, Positive-QTOFsplash10-0udi-0010900000-088577ac398d5035a83e2021-10-21Wishart 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 ID4292819
KEGG Compound IDNot Available
BioCyc IDNot Available
BiGG IDNot Available
Wikipedia LinkNot Available
METLIN IDNot Available
PubChem Compound5118005
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 ]