MiMeDB: Showing metabocard for (R)-2-hydroxyglutaryl-CoA (MMDBc0055028)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:40:16 UTC

Update Date

2025-10-07 16:08:52 UTC

Metabolite ID

MMDBc0055028

Metabolite Identification

Common Name

(R)-2-hydroxyglutaryl-CoA

Description

(R)-2-hydroxyglutaryl-CoA is a thioester metabolite belonging to the class of CoA derivatives. Its chemical structure features a hydroxyl group at the 2-position of the glutaryl moiety, making it a key intermediate in various biochemical pathways, particularly in the degradation of glutamate. This compound is primarily involved in the hydroxyglutarate pathway, where it undergoes dehydration to form (E)-glutaconyl-CoA, catalyzed by the enzyme 2-hydroxyglutaryl-CoA dehydratase from Acidaminococcus fermentans and Clostridium symbiosum (PMIDs: 21434666, 11980491). The dehydration process is a significant reaction, as it leads to further metabolic transformations, including decarboxylation to crotonyl-CoA (PMID: 11759672 ). Additionally, (R)-2-hydroxyglutaryl-CoA is generated from the activation of (R)-2-hydroxyglutarate in glutamate fermentation pathways (PMID: 9083111 ). The compound is also noted for its role in generating substrate-derived radicals during its enzymatic transformations (PMID: 15450487 ). Overall, (R)-2-hydroxyglutaryl-CoA serves as a crucial substrate in the metabolism of amino acids and contributes to energy production in anaerobic bacteria.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221402D          

 63 65  0  0  1  0            999 V2000
   16.5993   18.9509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7743   17.5220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8987   18.6490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1843   18.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6145   18.6490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3290   18.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4711   18.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7566   18.6490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.1881   17.8240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9013   17.8240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.3595   20.0043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.7189   20.6966    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6132   18.2365    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   21.9026   18.2365    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.9000   18.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4698   18.6490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.0246   20.9742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.2083   18.5140    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.6563   17.9009    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.4724   18.6490    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   24.7783   21.3097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9384   20.1537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7579   18.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.7958   19.2285    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.3277   18.6490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1868   18.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.8645   22.1302    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.1856   18.6490    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.0434   18.6490    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   25.4457   20.8248    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.6058   19.6688    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.2709   21.3097    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.1314   19.9822    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.6132   17.4115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.9000   17.4115    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.7553   18.2365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4698   19.4740    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   24.0288   18.4278    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.4724   19.4740    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.7579   17.4115    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    8.3277   19.4740    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.6627   17.1550    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   22.7668   15.9288    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   21.6016   15.9899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3467   18.5384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.1717   17.1095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7428   18.5384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.9178   17.1095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.4737   18.2365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.6158   18.2365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.9889   19.0570    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.8278   17.0939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.0447   17.4115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.2147   16.5419    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   19.7592   17.8240    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   18.3303   17.8240    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    9.0421   18.2365    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    7.6132   19.0615    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   21.9458   17.4126    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   23.5040   17.7438    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   22.4848   18.7079    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.4724   17.8240    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   23.6197   19.2717    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  5  1  0  0  0  0
  8  7  1  0  0  0  0
 13  3  1  0  0  0  0
 14  9  1  1  0  0  0
 15  5  1  0  0  0  0
 16  4  1  0  0  0  0
 19 14  1  0  0  0  0
 19 18  1  0  0  0  0
 21 17  2  0  0  0  0
 22 17  1  0  0  0  0
 23 20  1  0  0  0  0
 24 18  1  0  0  0  0
 25 13  1  0  0  0  0
 26  1  1  0  0  0  0
 26  2  1  0  0  0  0
 26 10  1  0  0  0  0
 26 20  1  0  0  0  0
 27 21  1  0  0  0  0
 28  7  1  4  0  0  0
 28 15  2  0  0  0  0
 29  6  1  4  0  0  0
 29 23  2  0  0  0  0
 30 11  2  0  0  0  0
 30 21  1  0  0  0  0
 31 11  1  0  0  0  0
 31 22  2  0  0  0  0
 32 12  2  0  0  0  0
 32 17  1  0  0  0  0
 33 12  1  0  0  0  0
 33 22  1  0  0  0  0
 24 33  1  1  0  0  0
 13 34  1  1  0  0  0
 35 15  1  0  0  0  0
 36 16  2  0  0  0  0
 37 16  1  0  0  0  0
 18 38  1  6  0  0  0
 20 39  1  1  0  0  0
 40 23  1  0  0  0  0
 41 25  2  0  0  0  0
 49  9  1  0  0  0  0
 50 10  1  0  0  0  0
 51 14  1  0  0  0  0
 51 24  1  0  0  0  0
 19 52  1  1  0  0  0
 54 42  1  0  0  0  0
 54 43  1  0  0  0  0
 54 44  2  0  0  0  0
 54 52  1  0  0  0  0
 55 45  1  0  0  0  0
 55 46  2  0  0  0  0
 55 49  1  0  0  0  0
 55 53  1  0  0  0  0
 56 47  1  0  0  0  0
 56 48  2  0  0  0  0
 56 50  1  0  0  0  0
 56 53  1  0  0  0  0
 57  8  1  0  0  0  0
 57 25  1  0  0  0  0
 13 58  1  1  0  0  0
 14 59  1  6  0  0  0
 18 60  1  1  0  0  0
 19 61  1  1  0  0  0
 20 62  1  1  0  0  0
 24 63  1  6  0  0  0
M  CHG  5  35  -1  37  -1  40  -1  42  -1  43  -1
M  END


  Mrv1652306172221402D          

 63 65  0  0  1  0            999 V2000
   16.5993   18.9509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.7743   17.5220    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.8987   18.6490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.1843   18.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.6145   18.6490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.3290   18.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.4711   18.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.7566   18.6490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.1881   17.8240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.9013   17.8240    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.3595   20.0043    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.7189   20.6966    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.6132   18.2365    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   21.9026   18.2365    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.9000   18.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.4698   18.6490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.0246   20.9742    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.2083   18.5140    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   22.6563   17.9009    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   15.4724   18.6490    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   24.7783   21.3097    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.9384   20.1537    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.7579   18.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.7958   19.2285    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.3277   18.6490    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.1868   18.2365    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.8645   22.1302    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   11.1856   18.6490    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   14.0434   18.6490    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   25.4457   20.8248    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.6058   19.6688    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.2709   21.3097    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   23.1314   19.9822    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    7.6132   17.4115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   11.9000   17.4115    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.7553   18.2365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.4698   19.4740    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   24.0288   18.4278    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.4724   19.4740    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.7579   17.4115    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    8.3277   19.4740    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.6627   17.1550    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   22.7668   15.9288    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   21.6016   15.9899    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.3467   18.5384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.1717   17.1095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.7428   18.5384    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.9178   17.1095    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   20.4737   18.2365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.6158   18.2365    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   21.9889   19.0570    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.8278   17.0939    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.0447   17.4115    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.2147   16.5419    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   19.7592   17.8240    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   18.3303   17.8240    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    9.0421   18.2365    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    7.6132   19.0615    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   21.9458   17.4126    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   23.5040   17.7438    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   22.4848   18.7079    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   15.4724   17.8240    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   23.6197   19.2717    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  4  3  1  0  0  0  0
  6  5  1  0  0  0  0
  8  7  1  0  0  0  0
 13  3  1  0  0  0  0
 14  9  1  1  0  0  0
 15  5  1  0  0  0  0
 16  4  1  0  0  0  0
 19 14  1  0  0  0  0
 19 18  1  0  0  0  0
 21 17  2  0  0  0  0
 22 17  1  0  0  0  0
 23 20  1  0  0  0  0
 24 18  1  0  0  0  0
 25 13  1  0  0  0  0
 26  1  1  0  0  0  0
 26  2  1  0  0  0  0
 26 10  1  0  0  0  0
 26 20  1  0  0  0  0
 27 21  1  0  0  0  0
 28  7  1  4  0  0  0
 28 15  2  0  0  0  0
 29  6  1  4  0  0  0
 29 23  2  0  0  0  0
 30 11  2  0  0  0  0
 30 21  1  0  0  0  0
 31 11  1  0  0  0  0
 31 22  2  0  0  0  0
 32 12  2  0  0  0  0
 32 17  1  0  0  0  0
 33 12  1  0  0  0  0
 33 22  1  0  0  0  0
 24 33  1  1  0  0  0
 13 34  1  1  0  0  0
 35 15  1  0  0  0  0
 36 16  2  0  0  0  0
 37 16  1  0  0  0  0
 18 38  1  6  0  0  0
 20 39  1  1  0  0  0
 40 23  1  0  0  0  0
 41 25  2  0  0  0  0
 49  9  1  0  0  0  0
 50 10  1  0  0  0  0
 51 14  1  0  0  0  0
 51 24  1  0  0  0  0
 19 52  1  1  0  0  0
 54 42  1  0  0  0  0
 54 43  1  0  0  0  0
 54 44  2  0  0  0  0
 54 52  1  0  0  0  0
 55 45  1  0  0  0  0
 55 46  2  0  0  0  0
 55 49  1  0  0  0  0
 55 53  1  0  0  0  0
 56 47  1  0  0  0  0
 56 48  2  0  0  0  0
 56 50  1  0  0  0  0
 56 53  1  0  0  0  0
 57  8  1  0  0  0  0
 57 25  1  0  0  0  0
 13 58  1  1  0  0  0
 14 59  1  6  0  0  0
 18 60  1  1  0  0  0
 19 61  1  1  0  0  0
 20 62  1  1  0  0  0
 24 63  1  6  0  0  0
M  CHG  5  35  -1  37  -1  40  -1  42  -1  43  -1
M  END
> <DATABASE_ID>
MMDBc0055028

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(CCC([O-])=O)C(=O)SCCN=C([O-])CCN=C([O-])[C@]([H])(O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])OP([O-])([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C26H42N7O20P3S/c1-26(2,20(39)23(40)29-6-5-15(35)28-7-8-57-25(41)13(34)3-4-16(36)37)10-50-56(47,48)53-55(45,46)49-9-14-19(52-54(42,43)44)18(38)24(51-14)33-12-32-17-21(27)30-11-31-22(17)33/h11-14,18-20,24,34,38-39H,3-10H2,1-2H3,(H,28,35)(H,29,40)(H,36,37)(H,45,46)(H,47,48)(H2,27,30,31)(H2,42,43,44)/p-5/t13-,14-,18-,19-,20+,24-/m1/s1

> <INCHI_KEY>
ITRSBJZNLOYNNR-WZZMXTMRSA-I

> <FORMULA>
C26H37N7O20P3S

> <MOLECULAR_WEIGHT>
892.6

> <EXACT_MASS>
892.105436687

> <JCHEM_ACCEPTOR_COUNT>
22

> <JCHEM_ATOM_COUNT>
94

> <JCHEM_AVERAGE_POLARIZABILITY>
78.20366595337835

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
-5

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(4R)-5-({2-[(3-{[(2R)-4-({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-2-hydroxy-3,3-dimethyl-1-oxidobutylidene]amino}-1-oxidopropylidene)amino]ethyl}sulfanyl)-4-hydroxy-5-oxopentanoate

> <JCHEM_LOGP>
-4.8488635849578126

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-5

> <JCHEM_PKA>
1.8878338596873014

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8192893038000357

> <JCHEM_PKA_STRONGEST_BASIC>
4.344294708434177

> <JCHEM_POLAR_SURFACE_AREA>
442.2900000000001

> <JCHEM_REFRACTIVITY>
219.93220000000008

> <JCHEM_ROTATABLE_BOND_COUNT>
24

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(4R)-5-({2-[(3-{[(2R)-4-[({[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-2-hydroxy-3,3-dimethyl-1-oxidobutylidene]amino}-1-oxidopropylidene)amino]ethyl}sulfanyl)-4-hydroxy-5-oxopentanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0      30.985  35.375   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      29.445  32.708   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      12.878  34.811   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      11.544  34.041   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      23.547  34.811   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      24.881  34.041   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      19.546  34.041   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      18.212  34.811   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      39.551  33.271   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      31.549  33.271   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      47.338  37.341   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      42.409  38.634   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      14.211  34.041   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      40.885  34.041   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      22.213  34.041   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      10.210  34.811   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      44.846  39.152   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      43.322  34.559   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      42.292  33.415   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0      28.882  34.811   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      46.253  39.778   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0      44.685  37.620   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      27.548  34.041   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      42.552  35.893   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0      15.545  34.811   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      30.215  34.041   0.000  0.00  0.00           C+0
HETATM   27  N   UNK     0      46.414  41.310   0.000  0.00  0.00           N+0
HETATM   28  N   UNK     0      20.880  34.811   0.000  0.00  0.00           N+0
HETATM   29  N   UNK     0      26.214  34.811   0.000  0.00  0.00           N+0
HETATM   30  N   UNK     0      47.499  38.873   0.000  0.00  0.00           N+0
HETATM   31  N   UNK     0      45.931  36.715   0.000  0.00  0.00           N+0
HETATM   32  N   UNK     0      43.439  39.778   0.000  0.00  0.00           N+0
HETATM   33  N   UNK     0      43.179  37.300   0.000  0.00  0.00           N+0
HETATM   34  O   UNK     0      14.211  32.501   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      22.213  32.501   0.000  0.00  0.00           O-1
HETATM   36  O   UNK     0       8.877  34.041   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0      10.210  36.351   0.000  0.00  0.00           O-1
HETATM   38  O   UNK     0      44.854  34.399   0.000  0.00  0.00           O+0
HETATM   39  O   UNK     0      28.882  36.351   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      27.548  32.501   0.000  0.00  0.00           O-1
HETATM   41  O   UNK     0      15.545  36.351   0.000  0.00  0.00           O+0
HETATM   42  O   UNK     0      40.437  32.023   0.000  0.00  0.00           O-1
HETATM   43  O   UNK     0      42.498  29.734   0.000  0.00  0.00           O-1
HETATM   44  O   UNK     0      40.323  29.848   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0      36.114  34.605   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0      37.654  31.938   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0      34.986  34.605   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0      33.446  31.938   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0      38.218  34.041   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      32.883  34.041   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      41.046  35.573   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0      42.612  31.909   0.000  0.00  0.00           O+0
HETATM   53  O   UNK     0      35.550  32.501   0.000  0.00  0.00           O+0
HETATM   54  P   UNK     0      41.467  30.878   0.000  0.00  0.00           P+0
HETATM   55  P   UNK     0      36.884  33.271   0.000  0.00  0.00           P+0
HETATM   56  P   UNK     0      34.216  33.271   0.000  0.00  0.00           P+0
HETATM   57  S   UNK     0      16.879  34.041   0.000  0.00  0.00           S+0
HETATM   58  H   UNK     0      14.211  35.581   0.000  0.00  0.00           H+0
HETATM   59  H   UNK     0      40.965  32.504   0.000  0.00  0.00           H+0
HETATM   60  H   UNK     0      43.874  33.122   0.000  0.00  0.00           H+0
HETATM   61  H   UNK     0      41.972  34.921   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0      28.882  33.271   0.000  0.00  0.00           H+0
HETATM   63  H   UNK     0      44.090  35.974   0.000  0.00  0.00           H+0
CONECT    1   26                                                            
CONECT    2   26                                                            
CONECT    3    4   13                                                       
CONECT    4    3   16                                                       
CONECT    5    6   15                                                       
CONECT    6    5   29                                                       
CONECT    7    8   28                                                       
CONECT    8    7   57                                                       
CONECT    9   14   49                                                       
CONECT   10   26   50                                                       
CONECT   11   30   31                                                       
CONECT   12   32   33                                                       
CONECT   13    3   25   34   58                                             
CONECT   14    9   19   51   59                                             
CONECT   15    5   28   35                                                  
CONECT   16    4   36   37                                                  
CONECT   17   21   22   32                                                  
CONECT   18   19   24   38   60                                             
CONECT   19   14   18   52   61                                             
CONECT   20   23   26   39   62                                             
CONECT   21   17   27   30                                                  
CONECT   22   17   31   33                                                  
CONECT   23   20   29   40                                                  
CONECT   24   18   33   51   63                                             
CONECT   25   13   41   57                                                  
CONECT   26    1    2   10   20                                             
CONECT   27   21                                                            
CONECT   28    7   15                                                       
CONECT   29    6   23                                                       
CONECT   30   11   21                                                       
CONECT   31   11   22                                                       
CONECT   32   12   17                                                       
CONECT   33   12   22   24                                                  
CONECT   34   13                                                            
CONECT   35   15                                                            
CONECT   36   16                                                            
CONECT   37   16                                                            
CONECT   38   18                                                            
CONECT   39   20                                                            
CONECT   40   23                                                            
CONECT   41   25                                                            
CONECT   42   54                                                            
CONECT   43   54                                                            
CONECT   44   54                                                            
CONECT   45   55                                                            
CONECT   46   55                                                            
CONECT   47   56                                                            
CONECT   48   56                                                            
CONECT   49    9   55                                                       
CONECT   50   10   56                                                       
CONECT   51   14   24                                                       
CONECT   52   19   54                                                       
CONECT   53   55   56                                                       
CONECT   54   42   43   44   52                                             
CONECT   55   45   46   49   53                                             
CONECT   56   47   48   50   53                                             
CONECT   57    8   25                                                       
CONECT   58   13                                                            
CONECT   59   14                                                            
CONECT   60   18                                                            
CONECT   61   19                                                            
CONECT   62   20                                                            
CONECT   63   24                                                            
MASTER        0    0    0    0    0    0    0    0   63    0  130    0
END

Synonyms

Not Available

Molecular Formula

C₂₆H₃₇N₇O₂₀P₃S

Average Mass

892.6

Monoisotopic Mass

892.105436687

IUPAC Name

(4R)-5-({2-[(3-{[(2R)-4-({[({[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy}(hydroxy)phosphoryl)oxy](hydroxy)phosphoryl}oxy)-2-hydroxy-3,3-dimethyl-1-oxidobutylidene]amino}-1-oxidopropylidene)amino]ethyl}sulfanyl)-4-hydroxy-5-oxopentanoate

Traditional Name

(4R)-5-({2-[(3-{[(2R)-4-[({[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-(phosphonooxy)oxolan-2-yl]methoxy(hydroxy)phosphoryl}oxy(hydroxy)phosphoryl)oxy]-2-hydroxy-3,3-dimethyl-1-oxidobutylidene]amino}-1-oxidopropylidene)amino]ethyl}sulfanyl)-4-hydroxy-5-oxopentanoate

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(CCC([O-])=O)C(=O)SCCN=C([O-])CCN=C([O-])[C@]([H])(O)C(C)(C)COP(O)(=O)OP(O)(=O)OC[C@@]1([H])O[C@@]([H])(N2C=NC3=C(N)N=CN=C23)[C@]([H])(O)[C@]1([H])OP([O-])([O-])=O

InChI Identifier

InChI=1S/C26H42N7O20P3S/c1-26(2,20(39)23(40)29-6-5-15(35)28-7-8-57-25(41)13(34)3-4-16(36)37)10-50-56(47,48)53-55(45,46)49-9-14-19(52-54(42,43)44)18(38)24(51-14)33-12-32-17-21(27)30-11-31-22(17)33/h11-14,18-20,24,34,38-39H,3-10H2,1-2H3,(H,28,35)(H,29,40)(H,36,37)(H,45,46)(H,47,48)(H2,27,30,31)(H2,42,43,44)/p-5/t13-,14-,18-,19-,20+,24-/m1/s1

InChI Key

ITRSBJZNLOYNNR-WZZMXTMRSA-I

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as 2,3,4-saturated fatty acyl coas. These are acyl-CoAs carrying a 2,3,4-saturated fatty acyl chain.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acyl thioesters

Direct Parent

2,3,4-saturated 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-5-phosphate
Pentose phosphate
Beta amino acid or derivatives
Glycosyl compound
N-glycosyl compound
Organic pyrophosphate
6-aminopurine
Monosaccharide phosphate
Purine
Imidazopyrimidine
Aminopyrimidine
Imidolactam
Monosaccharide
N-acyl-amine
Alkyl phosphate
N-substituted imidazole
Organic phosphoric acid derivative
Fatty amide
Pyrimidine
Phosphoric acid ester
Azole
Heteroaromatic compound
Imidazole
Oxolane
Secondary alcohol
Secondary carboxylic acid amide
Amino acid or derivatives
Thiocarboxylic acid ester
Carboxamide group
Carbothioic s-ester
Carboxylic acid salt
Amino acid
Thiocarboxylic acid or derivatives
Sulfenyl compound
Organoheterocyclic compound
Monocarboxylic acid or derivatives
Azacycle
Carboxylic acid derivative
Oxacycle
Carboxylic acid
Primary amine
Organosulfur compound
Hydrocarbon derivative
Alcohol
Amine
Carbonyl group
Organic oxide
Organic nitrogen compound
Organic oxygen compound
Organonitrogen compound
Organooxygen compound
Organic anion
Aromatic heteropolycyclic compound

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-4.8	ChemAxon
pKa (Strongest Acidic)	0.82	ChemAxon
pKa (Strongest Basic)	4.34	ChemAxon
Physiological Charge	-5	ChemAxon
Hydrogen Acceptor Count	22	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	442.29 Å²	ChemAxon
Rotatable Bond Count	24	ChemAxon
Refractivity	219.93 m³·mol⁻¹	ChemAxon
Polarizability	78.2 Å³	ChemAxon
Number of Rings	3	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	Yes	ChemAxon

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-21	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Microbial Pathways

Pathways

This table shows at most 5 pathways. For the full list of associated pathways:

See All Associated Bacterial Pathways

Name	SMPDB/PathBank	Species

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0038884	(R)-2-hydroxyglutaryl-CoA	D-2-Hydroxyglutaric acid	Thioesterase TesA	Hydrolysis	RHEA	34755880

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria/Eubacteria	Firmicutes	1	Pig ; Human feces

Exposure Sources

Other Exposures

Source Type	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

58163579

KEGG Compound ID

Not Available

BioCyc ID

2-HYDROXYGLUTARYL-COA

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

91819816

PDB ID

Not Available

ChEBI ID

132946

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for (R)-2-hydroxyglutaryl-CoA (MMDBc0055028)

MOL for #<Metabolite:0x0000564f9fbba338>

3D MOL for #<Metabolite:0x0000564f9fbba338>

3D SDF for #<Metabolite:0x0000564f9fbba338>

3D-SDF for #<Metabolite:0x0000564f9fbba338>

PDB for #<Metabolite:0x0000564f9fbba338>

3D PDB for #<Metabolite:0x0000564f9fbba338>

SMILES for #<Metabolite:0x0000564f9fbba338>

INCHI for #<Metabolite:0x0000564f9fbba338>

Structure for #<Metabolite:0x0000564f9fbba338>

3D Structure for #<Metabolite:0x0000564f9fbba338>