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Showing metabocard for Tridecanedioyl-CoA (HMDB0301135)

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Record Information
Version5.0
StatusPredicted
Creation Date2021-09-21 21:26:37 UTC
Update Date2021-10-01 16:52:49 UTC
HMDB IDHMDB0301135
Secondary Accession NumbersNone
Metabolite Identification
Common NameTridecanedioyl-CoA
DescriptionTridecanedioyl-coa is an acyl-CoA or acyl-coenzyme A. More specifically, it is a tridecanedioic acid thioester of coenzyme A. Tridecanedioyl-coa is an acyl-CoA with 13 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. Tridecanedioyl-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. Tridecanedioyl-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, Tridecanedioyl-CoA is transported into the mitochondria, the locus of beta oxidation. Transport of Tridecanedioyl-CoA into the mitochondria requires carnitine palmitoyltransferase 1 (CPT1), which converts Tridecanedioyl-CoA into Tridecanedioylcarnitine, which gets transported into the mitochondrial matrix. Once in the matrix, Tridecanedioylcarnitine is converted back to Tridecanedioyl-CoA by CPT2, whereupon beta-oxidation can begin. Beta oxidation of Tridecanedioyl-CoA occurs in four steps. First, since Tridecanedioyl-CoA is a long chain acyl-CoA it is the substrate for a long chain acyl-CoA dehydrogenase, which catalyzes dehydrogenation of Tridecanedioyl-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 Tridecanedioyl-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 HMDB0301135 (Tridecanedioyl-CoA)


  Mrv1652310101717572D          

 64 66  0  0  0  0            999 V2000
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M  END
Download

3D MOL for HMDB0301135 (Tridecanedioyl-CoA)

HMDB0301135
     RDKit          3D
Tridecanedioyl-CoA
122124  0  0  0  0  0  0  0  0999 V2000
   -1.6276   -1.5186   -0.3515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9046   -0.2466   -1.1113 C   0  0  0  0  0  0  0  0  0  0  0  0
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   16.4616    0.8547    1.7486 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7641   -0.5776    1.9671 C   0  0  0  0  0  0  0  0  0  0  0  0
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   16.9912   -1.0680    3.2671 O   0  0  0  0  0  0  0  0  0  0  0  0
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   -2.1696    0.2547   -3.1754 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9930   -1.4962   -2.9005 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.5528   -0.6241   -2.4095 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0722    1.5372   -0.9673 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5301    0.7913    0.6391 H   0  0  0  0  0  0  0  0  0  0  0  0
   -6.9556    0.7208   -0.9788 H   0  0  0  0  0  0  0  0  0  0  0  0
   -7.6841    2.5138    1.0633 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.8148    1.8108    1.8395 H   0  0  0  0  0  0  0  0  0  0  0  0
   -9.0961    1.3340    0.1959 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.7115   -0.5915    0.1128 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4864    2.8799    0.8965 H   0  0  0  0  0  0  0  0  0  0  0  0
  -15.0904    3.2827    0.6844 H   0  0  0  0  0  0  0  0  0  0  0  0
  -18.1844   -0.7434   -2.5992 H   0  0  0  0  0  0  0  0  0  0  0  0
  -17.8736    0.9950   -2.7997 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6390   -2.2763   -2.3841 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.7243    0.6720    2.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1057    1.4736    3.8660 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0125   -0.0358    2.7843 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6798   -3.1518    3.5852 H   0  0  0  0  0  0  0  0  0  0  0  0
  -10.1127   -1.2841    4.1668 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0091   -0.1994   -2.0156 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3955    1.6648   -2.8951 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2387    2.3579    1.1102 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6609   -0.2390    2.0497 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2516    1.3591    1.4991 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.1131   -0.2506    1.9699 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.4266   -1.4252    0.8373 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.7902    2.0906    0.8399 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.8745   -2.3067   -0.4229 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.2541   -1.9934   -1.1974 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6842   -3.3727   -2.6695 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.4244   -1.7005   -3.3935 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3764   -2.8719   -2.3977 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.3249   -4.0215   -1.0590 H   0  0  0  0  0  0  0  0  0  0  0  0
   10.6887   -2.2569   -0.2190 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1267   -2.2615    0.6101 H   0  0  0  0  0  0  0  0  0  0  0  0
    8.1863   -0.5230   -0.7350 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.6445    0.0178    0.1967 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.5732    1.0353   -1.9477 H   0  0  0  0  0  0  0  0  0  0  0  0
    9.1465   -0.4558   -2.7614 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.2913    0.1843   -3.4184 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.5178   -1.3126   -2.5213 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.3324    0.2105   -2.1389 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.2878    1.5707   -1.7109 H   0  0  0  0  0  0  0  0  0  0  0  0
   12.7528   -1.0235   -0.0888 H   0  0  0  0  0  0  0  0  0  0  0  0
   11.7341    0.4041    0.4589 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.8616    0.3669    1.4417 H   0  0  0  0  0  0  0  0  0  0  0  0
   13.5846    1.8484    0.4605 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.2643   -0.5848   -0.4166 H   0  0  0  0  0  0  0  0  0  0  0  0
   14.9927    0.8933   -1.3476 H   0  0  0  0  0  0  0  0  0  0  0  0
   16.0666    2.2788    0.1570 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.1203    0.9121   -0.2722 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.6291    1.1912    2.4049 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.3555    1.4272    2.0924 H   0  0  0  0  0  0  0  0  0  0  0  0
   17.8295   -0.8031    3.7892 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0
  2  3  1  0
  2  4  1  0
  4  5  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  6  9  1  0
  9 10  1  0
 10 11  2  0
 10 12  1  0
 10 13  1  0
 13 14  1  0
 14 15  1  0
 15 16  1  0
 16 17  1  0
 17 18  1  0
 18 19  1  0
 19 20  2  0
 20 21  1  0
 21 22  2  0
 22 23  1  0
 22 24  1  0
 24 25  2  0
 25 26  1  0
 26 27  2  0
 17 28  1  0
 28 29  1  0
 28 30  1  0
 30 31  1  0
 31 32  1  0
 32 33  2  0
 32 34  1  0
 32 35  1  0
  2 36  1  0
 36 37  1  0
 36 38  1  0
 38 39  1  0
 38 40  2  3
 40 41  1  0
 41 42  1  0
 42 43  1  0
 43 44  1  0
 43 45  2  3
 45 46  1  0
 46 47  1  0
 47 48  1  0
 48 49  1  0
 49 50  2  0
 49 51  1  0
 51 52  1  0
 52 53  1  0
 53 54  1  0
 54 55  1  0
 55 56  1  0
 56 57  1  0
 57 58  1  0
 58 59  1  0
 59 60  1  0
 60 61  1  0
 61 62  1  0
 62 63  2  0
 62 64  1  0
 30 15  1  0
 27 18  1  0
 27 21  1  0
  1 65  1  0
  1 66  1  0
  1 67  1  0
  3 68  1  0
  3 69  1  0
  3 70  1  0
  4 71  1  0
  4 72  1  0
  8 73  1  0
 12 74  1  0
 14 75  1  0
 14 76  1  0
 15 77  1  0
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 19 79  1  0
 23 80  1  0
 23 81  1  0
 25 82  1  0
 28 83  1  0
 29 84  1  0
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 34 86  1  0
 35 87  1  0
 36 88  1  0
 37 89  1  0
 39 90  1  0
 41 91  1  0
 41 92  1  0
 42 93  1  0
 42 94  1  0
 44 95  1  0
 46 96  1  0
 46 97  1  0
 47 98  1  0
 47 99  1  0
 51100  1  0
 51101  1  0
 52102  1  0
 52103  1  0
 53104  1  0
 53105  1  0
 54106  1  0
 54107  1  0
 55108  1  0
 55109  1  0
 56110  1  0
 56111  1  0
 57112  1  0
 57113  1  0
 58114  1  0
 58115  1  0
 59116  1  0
 59117  1  0
 60118  1  0
 60119  1  0
 61120  1  0
 61121  1  0
 64122  1  0
M  END
Download

3D SDF for HMDB0301135 (Tridecanedioyl-CoA)


  Mrv1652310101717572D          

 64 66  0  0  0  0            999 V2000
   24.6399   24.1726    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.8149   22.7436    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.0814   23.8706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.3670   23.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.7959   23.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.6525   23.8706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5104   23.8706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.9380   23.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2248   23.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.2235   23.8706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9393   23.8706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.5091   23.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6538   23.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.6551   23.8706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3695   23.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.5117   23.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.7972   23.8706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.2287   23.0456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.9419   23.0456    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   33.4000   25.2259    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.7595   25.9182    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.9432   23.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9406   23.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.7946   23.8706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3682   23.8706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.0652   26.1958    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.2489   23.7356    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.6969   23.1225    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5130   23.8706    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.8188   26.5313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   31.9789   25.3753    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.7985   23.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   30.8364   24.4501    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2274   23.4581    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   32.9051   27.3518    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.2261   23.8706    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.0840   23.8706    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   33.4863   26.0464    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   32.6464   24.8904    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   31.3115   26.5313    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   31.1720   25.2038    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   19.9406   22.6331    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.0801   23.4581    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.7946   24.6956    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3682   24.6956    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   32.0694   23.6494    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   23.5130   24.6956    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.7985   22.6331    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.7033   22.3766    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.8073   21.1504    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.6422   21.2115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.3873   23.7601    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.2123   22.3311    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.7833   23.7601    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.9583   22.3311    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.5143   23.4581    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.6564   23.4581    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.0294   24.2786    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.8684   22.3156    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.0853   22.6331    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.2553   21.7635    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   27.7998   23.0456    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   26.3708   23.0456    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   17.0827   23.4581    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  5  3  1  0  0  0  0
  6  4  1  0  0  0  0
  7  5  1  0  0  0  0
  8  6  1  0  0  0  0
  9  7  1  0  0  0  0
 10  8  1  0  0  0  0
 11  9  1  0  0  0  0
 12 10  1  0  0  0  0
 13 11  1  0  0  0  0
 15 14  1  0  0  0  0
 17 16  1  0  0  0  0
 22 18  1  0  0  0  0
 23 14  1  0  0  0  0
 24 12  1  0  0  0  0
 25 13  1  0  0  0  0
 28 22  1  0  0  0  0
 28 27  1  0  0  0  0
 30 26  2  0  0  0  0
 31 26  1  0  0  0  0
 32 29  1  0  0  0  0
 33 27  1  0  0  0  0
 34  1  1  0  0  0  0
 34  2  1  0  0  0  0
 34 19  1  0  0  0  0
 34 29  1  0  0  0  0
 35 30  1  0  0  0  0
 36 16  1  4  0  0  0
 36 23  2  0  0  0  0
 37 15  1  4  0  0  0
 37 32  2  0  0  0  0
 38 20  2  0  0  0  0
 38 30  1  0  0  0  0
 39 20  1  0  0  0  0
 39 31  2  0  0  0  0
 40 21  2  0  0  0  0
 40 26  1  0  0  0  0
 41 21  1  0  0  0  0
 41 31  1  0  0  0  0
 41 33  1  0  0  0  0
 42 23  1  0  0  0  0
 43 24  2  0  0  0  0
 44 24  1  0  0  0  0
 45 25  2  0  0  0  0
 46 27  1  0  0  0  0
 47 29  1  0  0  0  0
 48 32  1  0  0  0  0
 56 18  1  0  0  0  0
 57 19  1  0  0  0  0
 58 22  1  0  0  0  0
 58 33  1  0  0  0  0
 59 28  1  0  0  0  0
 61 49  1  0  0  0  0
 61 50  1  0  0  0  0
 61 51  2  0  0  0  0
 61 59  1  0  0  0  0
 62 52  1  0  0  0  0
 62 53  2  0  0  0  0
 62 56  1  0  0  0  0
 62 60  1  0  0  0  0
 63 54  1  0  0  0  0
 63 55  2  0  0  0  0
 63 57  1  0  0  0  0
 63 60  1  0  0  0  0
 64 17  1  0  0  0  0
 64 25  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0301135

> <DATABASE_NAME>
hmdb

> <SMILES>
CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)N1C=NC2=C(N)N=CN=C12)C(O)C(O)=NCCC(O)=NCCSC(=O)CCCCCCCCCCCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C34H58N7O19P3S/c1-34(2,29(47)32(48)37-15-14-23(42)36-16-17-64-25(45)13-11-9-7-5-3-4-6-8-10-12-24(43)44)19-57-63(54,55)60-62(52,53)56-18-22-28(59-61(49,50)51)27(46)33(58-22)41-21-40-26-30(35)38-20-39-31(26)41/h20-22,27-29,33,46-47H,3-19H2,1-2H3,(H,36,42)(H,37,48)(H,43,44)(H,52,53)(H,54,55)(H2,35,38,39)(H2,49,50,51)

> <INCHI_KEY>
PRMQICCZYHIFFX-UHFFFAOYSA-N

> <FORMULA>
C34H58N7O19P3S

> <MOLECULAR_WEIGHT>
993.85

> <EXACT_MASS>
993.272104844

> <JCHEM_ACCEPTOR_COUNT>
21

> <JCHEM_ATOM_COUNT>
122

> <JCHEM_AVERAGE_POLARIZABILITY>
94.27466565185276

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
10

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
13-({2-[(3-{[4-({[({[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-1,2-dihydroxy-3,3-dimethylbutylidene]amino}-1-hydroxypropylidene)amino]ethyl}sulfanyl)-13-oxotridecanoic acid

> <ALOGPS_LOGP>
1.17

> <JCHEM_LOGP>
-0.4209972309780541

> <ALOGPS_LOGS>
-2.31

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-5

> <JCHEM_PKA>
1.8913082167987971

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8196126593747106

> <JCHEM_PKA_STRONGEST_BASIC>
4.116365557823267

> <JCHEM_POLAR_SURFACE_AREA>
407.9100000000001

> <JCHEM_REFRACTIVITY>
225.5537000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
32

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
4.84e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
13-[(2-{[3-({4-[({[5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,2-dihydroxy-3,3-dimethylbutylidene}amino)-1-hydroxypropylidene]amino}ethyl)sulfanyl]-13-oxotridecanoic acid

> <JCHEM_VEBER_RULE>
0

$$$$
Download

3D-SDF for HMDB0301135 (Tridecanedioyl-CoA)

HMDB0301135
     RDKit          3D
Tridecanedioyl-CoA
122124  0  0  0  0  0  0  0  0999 V2000
   -1.6276   -1.5186   -0.3515 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9046   -0.2466   -1.1113 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4503   -0.5748   -2.5015 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.9022    0.6055   -0.3869 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.0987   -0.1058   -0.2501 O   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2799    0.7831    0.5304 P   0  0  0  0  0  5  0  0  0  0  0  0
   -4.6459    1.9824    1.2394 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.4045    1.4335   -0.5580 O   0  0  0  0  0  0  0  0  0  0  0  0
   -6.0747   -0.1574    1.6913 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.3822    0.7124    2.3566 P   0  0  0  0  0  5  0  0  0  0  0  0
   -7.2560    0.5642    3.8681 O   0  0  0  0  0  0  0  0  0  0  0  0
   -7.2447    2.3635    1.9537 O   0  0  0  0  0  0  0  0  0  0  0  0
   -8.8241    0.0604    1.8270 O   0  0  0  0  0  0  0  0  0  0  0  0
   -9.6006    0.9890    1.1245 C   0  0  0  0  0  0  0  0  0  0  0  0
  -10.9119    0.3391    0.6707 C   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6334    1.2834   -0.0091 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.6582    1.7699    0.7458 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.9442    1.5820    0.0537 N   0  0  0  0  0  0  0  0  0  0  0  0
  -15.0143    2.3737    0.1126 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.0099    1.8602   -0.6653 N   0  0  0  0  0  0  0  0  0  0  0  0
  -15.5585    0.7381   -1.2156 C   0  0  0  0  0  0  0  0  0  0  0  0
  -16.1758   -0.1536   -2.0804 C   0  0  0  0  0  0  0  0  0  0  0  0
  -17.5112    0.0508   -2.5270 N   0  0  0  0  0  0  0  0  0  0  0  0
  -15.4472   -1.2194   -2.4717 N   0  0  0  0  0  0  0  0  0  0  0  0
  -14.1876   -1.3999   -2.0400 C   0  0  0  0  0  0  0  0  0  0  0  0
  -13.6038   -0.5236   -1.2002 N   0  0  0  0  0  0  0  0  0  0  0  0
  -14.2592    0.5638   -0.7628 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.6942    1.0492    2.0694 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.3374    1.9735    3.0594 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.7003   -0.0494    1.9009 C   0  0  0  0  0  0  0  0  0  0  0  0
  -12.2190   -1.3178    1.8267 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.6469   -2.3649    2.9916 P   0  0  0  0  0  5  0  0  0  0  0  0
  -10.4608   -3.1064    2.3674 O   0  0  0  0  0  0  0  0  0  0  0  0
  -12.7485   -3.5054    3.5071 O   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0289   -1.5735    4.3526 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5949    0.4768   -1.3141 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7804    1.6662   -1.9963 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1756    0.6596   -0.0669 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3165    1.3530    1.0274 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.3602    0.1590    0.0261 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.1649    0.3002    1.2156 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5334   -0.3357    1.0371 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2251    0.3324   -0.0861 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4805    1.6865   -0.0203 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.6052   -0.3274   -1.1472 N   0  0  0  0  0  0  0  0  0  0  0  0
    4.3399   -1.7664   -1.2315 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.8721   -2.2754   -2.5416 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.6462   -2.0016   -2.6118 S   0  0  0  0  0  0  0  0  0  0  0  0
    7.5243   -2.9725   -1.4207 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8647   -3.6510   -0.6289 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.9868   -2.9832   -1.3619 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.6131   -2.0420   -0.3928 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.3516   -0.5892   -0.6432 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.8394   -0.0890   -1.9394 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.2409   -0.2144   -2.3278 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.3384    0.4343   -1.5985 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.5640    0.0521   -0.1929 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.7809    0.7764    0.4011 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.0541    0.4776   -0.3150 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.2290    1.2105    0.3188 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4616    0.8547    1.7486 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.7641   -0.5776    1.9671 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.8403   -1.4389    1.0528 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.9912   -1.0680    3.2671 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5612   -1.7483   -0.2343 H   0  0  0  0  0  0  0  0  0  0  0  0
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   -7.6841    2.5138    1.0633 H   0  0  0  0  0  0  0  0  0  0  0  0
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  -10.7115   -0.5915    0.1128 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.4864    2.8799    0.8965 H   0  0  0  0  0  0  0  0  0  0  0  0
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  -18.1844   -0.7434   -2.5992 H   0  0  0  0  0  0  0  0  0  0  0  0
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  -13.6390   -2.2763   -2.3841 H   0  0  0  0  0  0  0  0  0  0  0  0
  -13.7243    0.6720    2.2471 H   0  0  0  0  0  0  0  0  0  0  0  0
  -12.1057    1.4736    3.8660 H   0  0  0  0  0  0  0  0  0  0  0  0
  -11.0125   -0.0358    2.7843 H   0  0  0  0  0  0  0  0  0  0  0  0
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M  END
Download

PDB for HMDB0301135 (Tridecanedioyl-CoA)

HEADER    PROTEIN                                 10-OCT-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   10-OCT-17         0                                  
HETATM    1  C   UNK     0      45.995  45.122   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      44.455  42.455   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      22.552  44.558   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      21.218  43.788   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      23.886  43.788   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      19.885  44.558   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      25.219  44.558   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.551  43.788   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      26.553  43.788   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      17.217  44.558   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      27.887  44.558   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      15.884  43.788   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      29.220  43.788   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      38.556  44.558   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      39.890  43.788   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      34.555  43.788   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      33.221  44.558   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      54.560  43.018   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      46.558  43.018   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      62.347  47.088   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      57.418  48.381   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      55.894  43.788   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      37.222  43.788   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      14.550  44.558   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      30.554  44.558   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      59.855  48.899   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      58.331  44.307   0.000  0.00  0.00           C+0
HETATM   28  C   UNK     0      57.301  43.162   0.000  0.00  0.00           C+0
HETATM   29  C   UNK     0      43.891  44.558   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      61.262  49.525   0.000  0.00  0.00           C+0
HETATM   31  C   UNK     0      59.694  47.367   0.000  0.00  0.00           C+0
HETATM   32  C   UNK     0      42.557  43.788   0.000  0.00  0.00           C+0
HETATM   33  C   UNK     0      57.561  45.640   0.000  0.00  0.00           C+0
HETATM   34  C   UNK     0      45.225  43.788   0.000  0.00  0.00           C+0
HETATM   35  N   UNK     0      61.423  51.057   0.000  0.00  0.00           N+0
HETATM   36  N   UNK     0      35.889  44.558   0.000  0.00  0.00           N+0
HETATM   37  N   UNK     0      41.223  44.558   0.000  0.00  0.00           N+0
HETATM   38  N   UNK     0      62.508  48.620   0.000  0.00  0.00           N+0
HETATM   39  N   UNK     0      60.940  46.462   0.000  0.00  0.00           N+0
HETATM   40  N   UNK     0      58.448  49.525   0.000  0.00  0.00           N+0
HETATM   41  N   UNK     0      58.188  47.047   0.000  0.00  0.00           N+0
HETATM   42  O   UNK     0      37.222  42.248   0.000  0.00  0.00           O+0
HETATM   43  O   UNK     0      13.216  43.788   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      14.550  46.098   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0      30.554  46.098   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0      59.863  44.146   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0      43.891  46.098   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0      42.557  42.248   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      55.446  41.770   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      57.507  39.481   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      55.332  39.595   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      51.123  44.352   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      52.663  41.685   0.000  0.00  0.00           O+0
HETATM   54  O   UNK     0      49.996  44.352   0.000  0.00  0.00           O+0
HETATM   55  O   UNK     0      48.456  41.685   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      53.227  43.788   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      47.892  43.788   0.000  0.00  0.00           O+0
HETATM   58  O   UNK     0      56.055  45.320   0.000  0.00  0.00           O+0
HETATM   59  O   UNK     0      57.621  41.656   0.000  0.00  0.00           O+0
HETATM   60  O   UNK     0      50.559  42.248   0.000  0.00  0.00           O+0
HETATM   61  P   UNK     0      56.477  40.625   0.000  0.00  0.00           P+0
HETATM   62  P   UNK     0      51.893  43.018   0.000  0.00  0.00           P+0
HETATM   63  P   UNK     0      49.226  43.018   0.000  0.00  0.00           P+0
HETATM   64  S   UNK     0      31.888  43.788   0.000  0.00  0.00           S+0
CONECT    1   34                                                            
CONECT    2   34                                                            
CONECT    3    4    5                                                       
CONECT    4    3    6                                                       
CONECT    5    3    7                                                       
CONECT    6    4    8                                                       
CONECT    7    5    9                                                       
CONECT    8    6   10                                                       
CONECT    9    7   11                                                       
CONECT   10    8   12                                                       
CONECT   11    9   13                                                       
CONECT   12   10   24                                                       
CONECT   13   11   25                                                       
CONECT   14   15   23                                                       
CONECT   15   14   37                                                       
CONECT   16   17   36                                                       
CONECT   17   16   64                                                       
CONECT   18   22   56                                                       
CONECT   19   34   57                                                       
CONECT   20   38   39                                                       
CONECT   21   40   41                                                       
CONECT   22   18   28   58                                                  
CONECT   23   14   36   42                                                  
CONECT   24   12   43   44                                                  
CONECT   25   13   45   64                                                  
CONECT   26   30   31   40                                                  
CONECT   27   28   33   46                                                  
CONECT   28   22   27   59                                                  
CONECT   29   32   34   47                                                  
CONECT   30   26   35   38                                                  
CONECT   31   26   39   41                                                  
CONECT   32   29   37   48                                                  
CONECT   33   27   41   58                                                  
CONECT   34    1    2   19   29                                             
CONECT   35   30                                                            
CONECT   36   16   23                                                       
CONECT   37   15   32                                                       
CONECT   38   20   30                                                       
CONECT   39   20   31                                                       
CONECT   40   21   26                                                       
CONECT   41   21   31   33                                                  
CONECT   42   23                                                            
CONECT   43   24                                                            
CONECT   44   24                                                            
CONECT   45   25                                                            
CONECT   46   27                                                            
CONECT   47   29                                                            
CONECT   48   32                                                            
CONECT   49   61                                                            
CONECT   50   61                                                            
CONECT   51   61                                                            
CONECT   52   62                                                            
CONECT   53   62                                                            
CONECT   54   63                                                            
CONECT   55   63                                                            
CONECT   56   18   62                                                       
CONECT   57   19   63                                                       
CONECT   58   22   33                                                       
CONECT   59   28   61                                                       
CONECT   60   62   63                                                       
CONECT   61   49   50   51   59                                             
CONECT   62   52   53   56   60                                             
CONECT   63   54   55   57   60                                             
CONECT   64   17   25                                                       
MASTER        0    0    0    0    0    0    0    0   64    0  132    0
END
Download

3D PDB for HMDB0301135 (Tridecanedioyl-CoA)

COMPND    HMDB0301135
HETATM    1  C1  UNL     1      -1.628  -1.519  -0.352  1.00  0.00           C  
HETATM    2  C2  UNL     1      -1.905  -0.247  -1.111  1.00  0.00           C  
HETATM    3  C3  UNL     1      -2.450  -0.575  -2.502  1.00  0.00           C  
HETATM    4  C4  UNL     1      -2.902   0.606  -0.387  1.00  0.00           C  
HETATM    5  O1  UNL     1      -4.099  -0.106  -0.250  1.00  0.00           O  
HETATM    6  P1  UNL     1      -5.280   0.783   0.530  1.00  0.00           P  
HETATM    7  O2  UNL     1      -4.646   1.982   1.239  1.00  0.00           O  
HETATM    8  O3  UNL     1      -6.405   1.434  -0.558  1.00  0.00           O  
HETATM    9  O4  UNL     1      -6.075  -0.157   1.691  1.00  0.00           O  
HETATM   10  P2  UNL     1      -7.382   0.712   2.357  1.00  0.00           P  
HETATM   11  O5  UNL     1      -7.256   0.564   3.868  1.00  0.00           O  
HETATM   12  O6  UNL     1      -7.245   2.364   1.954  1.00  0.00           O  
HETATM   13  O7  UNL     1      -8.824   0.060   1.827  1.00  0.00           O  
HETATM   14  C5  UNL     1      -9.601   0.989   1.124  1.00  0.00           C  
HETATM   15  C6  UNL     1     -10.912   0.339   0.671  1.00  0.00           C  
HETATM   16  O8  UNL     1     -11.633   1.283  -0.009  1.00  0.00           O  
HETATM   17  C7  UNL     1     -12.658   1.770   0.746  1.00  0.00           C  
HETATM   18  N1  UNL     1     -13.944   1.582   0.054  1.00  0.00           N  
HETATM   19  C8  UNL     1     -15.014   2.374   0.113  1.00  0.00           C  
HETATM   20  N2  UNL     1     -16.010   1.860  -0.665  1.00  0.00           N  
HETATM   21  C9  UNL     1     -15.558   0.738  -1.216  1.00  0.00           C  
HETATM   22  C10 UNL     1     -16.176  -0.154  -2.080  1.00  0.00           C  
HETATM   23  N3  UNL     1     -17.511   0.051  -2.527  1.00  0.00           N  
HETATM   24  N4  UNL     1     -15.447  -1.219  -2.472  1.00  0.00           N  
HETATM   25  C11 UNL     1     -14.188  -1.400  -2.040  1.00  0.00           C  
HETATM   26  N5  UNL     1     -13.604  -0.524  -1.200  1.00  0.00           N  
HETATM   27  C12 UNL     1     -14.259   0.564  -0.763  1.00  0.00           C  
HETATM   28  C13 UNL     1     -12.694   1.049   2.069  1.00  0.00           C  
HETATM   29  O9  UNL     1     -12.337   1.973   3.059  1.00  0.00           O  
HETATM   30  C14 UNL     1     -11.700  -0.049   1.901  1.00  0.00           C  
HETATM   31  O10 UNL     1     -12.219  -1.318   1.827  1.00  0.00           O  
HETATM   32  P3  UNL     1     -11.647  -2.365   2.992  1.00  0.00           P  
HETATM   33  O11 UNL     1     -10.461  -3.106   2.367  1.00  0.00           O  
HETATM   34  O12 UNL     1     -12.748  -3.505   3.507  1.00  0.00           O  
HETATM   35  O13 UNL     1     -11.029  -1.573   4.353  1.00  0.00           O  
HETATM   36  C15 UNL     1      -0.595   0.477  -1.314  1.00  0.00           C  
HETATM   37  O14 UNL     1      -0.780   1.666  -1.996  1.00  0.00           O  
HETATM   38  C16 UNL     1       0.176   0.660  -0.067  1.00  0.00           C  
HETATM   39  O15 UNL     1      -0.316   1.353   1.027  1.00  0.00           O  
HETATM   40  N6  UNL     1       1.360   0.159   0.026  1.00  0.00           N  
HETATM   41  C17 UNL     1       2.165   0.300   1.216  1.00  0.00           C  
HETATM   42  C18 UNL     1       3.533  -0.336   1.037  1.00  0.00           C  
HETATM   43  C19 UNL     1       4.225   0.332  -0.086  1.00  0.00           C  
HETATM   44  O16 UNL     1       4.481   1.686  -0.020  1.00  0.00           O  
HETATM   45  N7  UNL     1       4.605  -0.327  -1.147  1.00  0.00           N  
HETATM   46  C20 UNL     1       4.340  -1.766  -1.232  1.00  0.00           C  
HETATM   47  C21 UNL     1       4.872  -2.275  -2.542  1.00  0.00           C  
HETATM   48  S1  UNL     1       6.646  -2.002  -2.612  1.00  0.00           S  
HETATM   49  C22 UNL     1       7.524  -2.973  -1.421  1.00  0.00           C  
HETATM   50  O17 UNL     1       6.865  -3.651  -0.629  1.00  0.00           O  
HETATM   51  C23 UNL     1       8.987  -2.983  -1.362  1.00  0.00           C  
HETATM   52  C24 UNL     1       9.613  -2.042  -0.393  1.00  0.00           C  
HETATM   53  C25 UNL     1       9.352  -0.589  -0.643  1.00  0.00           C  
HETATM   54  C26 UNL     1       9.839  -0.089  -1.939  1.00  0.00           C  
HETATM   55  C27 UNL     1      11.241  -0.214  -2.328  1.00  0.00           C  
HETATM   56  C28 UNL     1      12.338   0.434  -1.599  1.00  0.00           C  
HETATM   57  C29 UNL     1      12.564   0.052  -0.193  1.00  0.00           C  
HETATM   58  C30 UNL     1      13.781   0.776   0.401  1.00  0.00           C  
HETATM   59  C31 UNL     1      15.054   0.478  -0.315  1.00  0.00           C  
HETATM   60  C32 UNL     1      16.229   1.211   0.319  1.00  0.00           C  
HETATM   61  C33 UNL     1      16.462   0.855   1.749  1.00  0.00           C  
HETATM   62  C34 UNL     1      16.764  -0.578   1.967  1.00  0.00           C  
HETATM   63  O18 UNL     1      16.840  -1.439   1.053  1.00  0.00           O  
HETATM   64  O19 UNL     1      16.991  -1.068   3.267  1.00  0.00           O  
HETATM   65  H1  UNL     1      -0.561  -1.748  -0.234  1.00  0.00           H  
HETATM   66  H2  UNL     1      -2.084  -2.372  -0.929  1.00  0.00           H  
HETATM   67  H3  UNL     1      -2.098  -1.467   0.666  1.00  0.00           H  
HETATM   68  H4  UNL     1      -2.170   0.255  -3.175  1.00  0.00           H  
HETATM   69  H5  UNL     1      -1.993  -1.496  -2.901  1.00  0.00           H  
HETATM   70  H6  UNL     1      -3.553  -0.624  -2.409  1.00  0.00           H  
HETATM   71  H7  UNL     1      -3.072   1.537  -0.967  1.00  0.00           H  
HETATM   72  H8  UNL     1      -2.530   0.791   0.639  1.00  0.00           H  
HETATM   73  H9  UNL     1      -6.956   0.721  -0.979  1.00  0.00           H  
HETATM   74  H10 UNL     1      -7.684   2.514   1.063  1.00  0.00           H  
HETATM   75  H11 UNL     1      -9.815   1.811   1.840  1.00  0.00           H  
HETATM   76  H12 UNL     1      -9.096   1.334   0.196  1.00  0.00           H  
HETATM   77  H13 UNL     1     -10.711  -0.591   0.113  1.00  0.00           H  
HETATM   78  H14 UNL     1     -12.486   2.880   0.897  1.00  0.00           H  
HETATM   79  H15 UNL     1     -15.090   3.283   0.684  1.00  0.00           H  
HETATM   80  H16 UNL     1     -18.184  -0.743  -2.599  1.00  0.00           H  
HETATM   81  H17 UNL     1     -17.874   0.995  -2.800  1.00  0.00           H  
HETATM   82  H18 UNL     1     -13.639  -2.276  -2.384  1.00  0.00           H  
HETATM   83  H19 UNL     1     -13.724   0.672   2.247  1.00  0.00           H  
HETATM   84  H20 UNL     1     -12.106   1.474   3.866  1.00  0.00           H  
HETATM   85  H21 UNL     1     -11.012  -0.036   2.784  1.00  0.00           H  
HETATM   86  H22 UNL     1     -13.680  -3.152   3.585  1.00  0.00           H  
HETATM   87  H23 UNL     1     -10.113  -1.284   4.167  1.00  0.00           H  
HETATM   88  H24 UNL     1      -0.009  -0.199  -2.016  1.00  0.00           H  
HETATM   89  H25 UNL     1      -0.395   1.665  -2.895  1.00  0.00           H  
HETATM   90  H26 UNL     1      -0.239   2.358   1.110  1.00  0.00           H  
HETATM   91  H27 UNL     1       1.661  -0.239   2.050  1.00  0.00           H  
HETATM   92  H28 UNL     1       2.252   1.359   1.499  1.00  0.00           H  
HETATM   93  H29 UNL     1       4.113  -0.251   1.970  1.00  0.00           H  
HETATM   94  H30 UNL     1       3.427  -1.425   0.837  1.00  0.00           H  
HETATM   95  H31 UNL     1       4.790   2.091   0.840  1.00  0.00           H  
HETATM   96  H32 UNL     1       4.874  -2.307  -0.423  1.00  0.00           H  
HETATM   97  H33 UNL     1       3.254  -1.993  -1.197  1.00  0.00           H  
HETATM   98  H34 UNL     1       4.684  -3.373  -2.670  1.00  0.00           H  
HETATM   99  H35 UNL     1       4.424  -1.701  -3.393  1.00  0.00           H  
HETATM  100  H36 UNL     1       9.376  -2.872  -2.398  1.00  0.00           H  
HETATM  101  H37 UNL     1       9.325  -4.022  -1.059  1.00  0.00           H  
HETATM  102  H38 UNL     1      10.689  -2.257  -0.219  1.00  0.00           H  
HETATM  103  H39 UNL     1       9.127  -2.262   0.610  1.00  0.00           H  
HETATM  104  H40 UNL     1       8.186  -0.523  -0.735  1.00  0.00           H  
HETATM  105  H41 UNL     1       9.644   0.018   0.197  1.00  0.00           H  
HETATM  106  H42 UNL     1       9.573   1.035  -1.948  1.00  0.00           H  
HETATM  107  H43 UNL     1       9.146  -0.456  -2.761  1.00  0.00           H  
HETATM  108  H44 UNL     1      11.291   0.184  -3.418  1.00  0.00           H  
HETATM  109  H45 UNL     1      11.518  -1.313  -2.521  1.00  0.00           H  
HETATM  110  H46 UNL     1      13.332   0.211  -2.139  1.00  0.00           H  
HETATM  111  H47 UNL     1      12.288   1.571  -1.711  1.00  0.00           H  
HETATM  112  H48 UNL     1      12.753  -1.023  -0.089  1.00  0.00           H  
HETATM  113  H49 UNL     1      11.734   0.404   0.459  1.00  0.00           H  
HETATM  114  H50 UNL     1      13.862   0.367   1.442  1.00  0.00           H  
HETATM  115  H51 UNL     1      13.585   1.848   0.461  1.00  0.00           H  
HETATM  116  H52 UNL     1      15.264  -0.585  -0.417  1.00  0.00           H  
HETATM  117  H53 UNL     1      14.993   0.893  -1.348  1.00  0.00           H  
HETATM  118  H54 UNL     1      16.067   2.279   0.157  1.00  0.00           H  
HETATM  119  H55 UNL     1      17.120   0.912  -0.272  1.00  0.00           H  
HETATM  120  H56 UNL     1      15.629   1.191   2.405  1.00  0.00           H  
HETATM  121  H57 UNL     1      17.356   1.427   2.092  1.00  0.00           H  
HETATM  122  H58 UNL     1      17.829  -0.803   3.789  1.00  0.00           H  
CONECT    1    2   65   66   67
CONECT    2    3    4   36
CONECT    3   68   69   70
CONECT    4    5   71   72
CONECT    5    6
CONECT    6    7    7    8    9
CONECT    8   73
CONECT    9   10
CONECT   10   11   11   12   13
CONECT   12   74
CONECT   13   14
CONECT   14   15   75   76
CONECT   15   16   30   77
CONECT   16   17
CONECT   17   18   28   78
CONECT   18   19   27
CONECT   19   20   20   79
CONECT   20   21
CONECT   21   22   22   27
CONECT   22   23   24
CONECT   23   80   81
CONECT   24   25   25
CONECT   25   26   82
CONECT   26   27   27
CONECT   28   29   30   83
CONECT   29   84
CONECT   30   31   85
CONECT   31   32
CONECT   32   33   33   34   35
CONECT   34   86
CONECT   35   87
CONECT   36   37   38   88
CONECT   37   89
CONECT   38   39   40   40
CONECT   39   90
CONECT   40   41
CONECT   41   42   91   92
CONECT   42   43   93   94
CONECT   43   44   45   45
CONECT   44   95
CONECT   45   46
CONECT   46   47   96   97
CONECT   47   48   98   99
CONECT   48   49
CONECT   49   50   50   51
CONECT   51   52  100  101
CONECT   52   53  102  103
CONECT   53   54  104  105
CONECT   54   55  106  107
CONECT   55   56  108  109
CONECT   56   57  110  111
CONECT   57   58  112  113
CONECT   58   59  114  115
CONECT   59   60  116  117
CONECT   60   61  118  119
CONECT   61   62  120  121
CONECT   62   63   63   64
CONECT   64  122
END
Download

SMILES for HMDB0301135 (Tridecanedioyl-CoA)

CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)N1C=NC2=C(N)N=CN=C12)C(O)C(O)=NCCC(O)=NCCSC(=O)CCCCCCCCCCCC(O)=O
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INCHI for HMDB0301135 (Tridecanedioyl-CoA)

InChI=1S/C34H58N7O19P3S/c1-34(2,29(47)32(48)37-15-14-23(42)36-16-17-64-25(45)13-11-9-7-5-3-4-6-8-10-12-24(43)44)19-57-63(54,55)60-62(52,53)56-18-22-28(59-61(49,50)51)27(46)33(58-22)41-21-40-26-30(35)38-20-39-31(26)41/h20-22,27-29,33,46-47H,3-19H2,1-2H3,(H,36,42)(H,37,48)(H,43,44)(H,52,53)(H,54,55)(H2,35,38,39)(H2,49,50,51)
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View in JSmolView Stereo Labels
Synonyms
ValueSource
13-({2-[(3-{[4-({[({[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-1,2-dihydroxy-3,3-dimethylbutylidene]amino}-1-hydroxypropylidene)amino]ethyl}sulfanyl)-13-oxotridecanoateGenerator
13-({2-[(3-{[4-({[({[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-1,2-dihydroxy-3,3-dimethylbutylidene]amino}-1-hydroxypropylidene)amino]ethyl}sulphanyl)-13-oxotridecanoateGenerator
13-({2-[(3-{[4-({[({[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-1,2-dihydroxy-3,3-dimethylbutylidene]amino}-1-hydroxypropylidene)amino]ethyl}sulphanyl)-13-oxotridecanoic acidGenerator
Chemical FormulaC34H58N7O19P3S
Average Molecular Weight993.85
Monoisotopic Molecular Weight993.272104844
IUPAC Name13-({2-[(3-{[4-({[({[5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-1,2-dihydroxy-3,3-dimethylbutylidene]amino}-1-hydroxypropylidene)amino]ethyl}sulfanyl)-13-oxotridecanoic acid
Traditional Name13-[(2-{[3-({4-[({[5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-1,2-dihydroxy-3,3-dimethylbutylidene}amino)-1-hydroxypropylidene]amino}ethyl)sulfanyl]-13-oxotridecanoic acid
CAS Registry NumberNot Available
SMILES
CC(C)(COP(O)(=O)OP(O)(=O)OCC1OC(C(O)C1OP(O)(O)=O)N1C=NC2=C(N)N=CN=C12)C(O)C(O)=NCCC(O)=NCCSC(=O)CCCCCCCCCCCC(O)=O
InChI Identifier
InChI=1S/C34H58N7O19P3S/c1-34(2,29(47)32(48)37-15-14-23(42)36-16-17-64-25(45)13-11-9-7-5-3-4-6-8-10-12-24(43)44)19-57-63(54,55)60-62(52,53)56-18-22-28(59-61(49,50)51)27(46)33(58-22)41-21-40-26-30(35)38-20-39-31(26)41/h20-22,27-29,33,46-47H,3-19H2,1-2H3,(H,36,42)(H,37,48)(H,43,44)(H,52,53)(H,54,55)(H2,35,38,39)(H2,49,50,51)
InChI KeyPRMQICCZYHIFFX-UHFFFAOYSA-N
Chemical Taxonomy
Description Belongs to the class of organic compounds known as long-chain fatty acyl coas. These are acyl CoAs where the group acylated to the coenzyme A moiety is a long aliphatic chain of 13 to 21 carbon atoms.
KingdomOrganic compounds
Super ClassLipids and lipid-like molecules
ClassFatty Acyls
Sub ClassFatty acyl thioesters
Direct ParentLong-chain fatty acyl CoAs
Alternative Parents
Substituents
  • Coenzyme a or derivatives
  • Purine ribonucleoside 3',5'-bisphosphate
  • Purine ribonucleoside bisphosphate
  • Purine ribonucleoside diphosphate
  • Ribonucleoside 3'-phosphate
  • Pentose phosphate
  • Pentose-5-phosphate
  • Long-chain fatty acid
  • Glycosyl compound
  • N-glycosyl compound
  • 6-aminopurine
  • Monosaccharide phosphate
  • Organic pyrophosphate
  • Pentose monosaccharide
  • Imidazopyrimidine
  • Purine
  • Aminopyrimidine
  • Hydroxy fatty acid
  • Monoalkyl phosphate
  • Alkyl phosphate
  • Monosaccharide
  • N-substituted imidazole
  • Organic phosphoric acid derivative
  • Fatty acid
  • Phosphoric acid ester
  • Imidolactam
  • Pyrimidine
  • Azole
  • Tetrahydrofuran
  • Imidazole
  • Heteroaromatic compound
  • Thiocarboxylic acid ester
  • Secondary alcohol
  • Carbothioic s-ester
  • Amino acid
  • Amino acid or derivatives
  • Thiocarboxylic acid or derivatives
  • Organoheterocyclic compound
  • Propargyl-type 1,3-dipolar organic compound
  • Organic 1,3-dipolar compound
  • Carboximidic acid
  • Carboximidic acid derivative
  • Carboxylic acid derivative
  • Carboxylic acid
  • Azacycle
  • Monocarboxylic acid or derivatives
  • Sulfenyl compound
  • Oxacycle
  • Organic oxygen compound
  • Organopnictogen compound
  • Organic oxide
  • Alcohol
  • Carbonyl group
  • Organosulfur compound
  • Hydrocarbon derivative
  • Organooxygen compound
  • Amine
  • Primary amine
  • Organonitrogen compound
  • Organic nitrogen compound
  • 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
logP1.17ALOGPS
logP-0.42ChemAxon
logS-2.3ALOGPS
pKa (Strongest Acidic)0.82ChemAxon
pKa (Strongest Basic)4.12ChemAxon
Physiological Charge-5ChemAxon
Hydrogen Acceptor Count21ChemAxon
Hydrogen Donor Count10ChemAxon
Polar Surface Area407.91 ŲChemAxon
Rotatable Bond Count32ChemAxon
Refractivity225.55 m³·mol⁻¹ChemAxon
Polarizability94.27 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]+283.71532859911
AllCCS[M+H-H2O]+284.41932859911
AllCCS[M+Na]+282.80832859911
AllCCS[M+NH4]+283.01732859911
AllCCS[M-H]-292.48932859911
AllCCS[M+Na-2H]-298.04232859911
AllCCS[M+HCOO]-304.11232859911
DeepCCS[M-2H]-321.75530932474
DeepCCS[M+Na]+295.77130932474

Predicted Kovats Retention Indices

Not Available
Spectra

MS/MS Spectra

Spectrum TypeDescriptionSplash KeyDeposition DateSourceView
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanedioyl-CoA 10V, Positive-QTOFsplash10-000i-1918100305-7d9901cfd09f62a287882018-04-05Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanedioyl-CoA 20V, Positive-QTOFsplash10-000i-0927200000-78e27f653feeed33878f2018-04-05Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanedioyl-CoA 40V, Positive-QTOFsplash10-000i-1903000000-f5fb44ad6abe239fb71c2018-04-05Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanedioyl-CoA 10V, Negative-QTOFsplash10-0059-4951343508-b670b498173ef018148a2018-04-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanedioyl-CoA 20V, Negative-QTOFsplash10-003r-3911201001-9622501a0706b4fa58b52018-04-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanedioyl-CoA 40V, Negative-QTOFsplash10-057i-5900100000-03072edecbbea71400272018-04-06Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanedioyl-CoA 10V, Positive-QTOFsplash10-056u-1000000009-a467a4b9dfa5d916d4ac2021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanedioyl-CoA 20V, Positive-QTOFsplash10-0a4i-9000200028-064492869c4fdf522b182021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanedioyl-CoA 40V, Positive-QTOFsplash10-000i-0000900000-199945a5e358010087e02021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanedioyl-CoA 10V, Negative-QTOFsplash10-0006-0000000009-5443a63d8e3113ea4d072021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanedioyl-CoA 20V, Negative-QTOFsplash10-00dl-5020000109-e9bb35c00d9a2b5a41372021-10-21Wishart LabView Spectrum
Predicted LC-MS/MSPredicted LC-MS/MS Spectrum - Tridecanedioyl-CoA 40V, Negative-QTOFsplash10-002f-7012211091-08ce47e4e7caaef9ac902021-10-21Wishart 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 ]