MiMeDB: Showing metabocard for 2-Hydroxyglutaryl-CoA (MMDBc0049880)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:45:26 UTC

Update Date

2025-10-07 16:08:14 UTC

Metabolite ID

MMDBc0049880

Metabolite Identification

Common Name

2-Hydroxyglutaryl-CoA

Description

2-Hydroxyglutaryl-CoA is a thioester metabolite belonging to the class of CoA derivatives. Its chemical structure features a hydroxy group at the second carbon of the glutaryl moiety, which is crucial for its biochemical reactivity. This compound plays a significant role in anaerobic metabolic pathways, particularly in the gut microbiome, where it is involved in the degradation of 4-hydroxynonanedioic acid through β-oxidation, leading to the formation of 2-ketoglutaric acid that enters the citric acid cycle (PMID:25274632 ). The enzyme 2-hydroxyglutaryl-CoA dehydratase, derived from Clostridium symbiosum, catalyzes the reversible dehydration of (R)-2-hydroxyglutaryl-CoA to (E)-glutaconyl-CoA, highlighting its importance in metabolic conversions (PMID:21434666 ). Additionally, the enzyme's structure is related to the ASKHA superfamily of phosphotransferases, sharing a common fold with pantothenate kinase (PMID:24311585 ). Its substrate specificity and the role in producing bio-based compounds like adipic acid further emphasize its relevance in biotechnological applications (PMID:21434666 ). The unique properties of 2-hydroxyglutaryl-CoA and its associated enzymes underscore its significance in microbial metabolism and potential industrial uses.

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006051501022D          
 
 57 59  0  0  1  0            999 V2000
   18.5345  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.2490  -19.9650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9634  -20.3775    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   20.6779  -19.9650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3924  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.1068  -19.9650    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.8213  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5358  -19.9650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2502  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.9647  -19.9650    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   25.6792  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.3936  -19.9650    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   27.1081  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.8226  -19.9650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.5370  -20.3775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.2490  -19.1401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.8213  -21.2024    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.6792  -21.2023    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.3936  -19.1400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.1081  -19.5525    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.1081  -21.2025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.3620  -20.3775    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   30.1870  -20.3775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.3620  -21.2025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.5338  -17.4488    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   26.3588  -17.4488    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   26.6137  -16.6641    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   25.9463  -16.1792    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.2788  -16.6641    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   27.3913  -16.4114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.0488  -18.1162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.8437  -18.1162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.6687  -18.1162    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   27.6687  -17.2912    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.4937  -18.1162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.6687  -18.9412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.8525  -15.5925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.8525  -16.4175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2815  -16.4175    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.2815  -15.5925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5670  -15.1800    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.1381  -15.1800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.4235  -15.5925    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.4235  -16.4175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.1381  -16.8300    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.1381  -14.3551    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   28.5594  -16.6662    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.3844  -16.6662    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   29.3844  -15.8412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.2094  -16.6662    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.3844  -18.5637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8068  -19.9650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0923  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3778  -19.9650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6634  -20.3775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5377  -21.2023    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3778  -19.1400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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  1  0  0  0  0
  8  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  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  2 16  2  0  0  0  0
  7 17  2  0  0  0  0
 11 18  2  0  0  0  0
 12 19  1  6  0  0  0
 13 20  1  0  0  0  0
 13 21  1  0  0  0  0
 15 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 25 29  1  0  0  0  0
 27 30  1  6  0  0  0
 25 31  1  1  0  0  0
 26 32  1  1  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
 33 36  2  0  0  0  0
 37 38  2  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  2  0  0  0  0
 37 41  1  0  0  0  0
 37 42  1  0  0  0  0
 42 43  2  0  0  0  0
 43 44  1  0  0  0  0
 44 45  2  0  0  0  0
 38 45  1  0  0  0  0
 42 46  1  0  0  0  0
 29 39  1  6  0  0  0
 30 47  1  0  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 48 50  2  0  0  0  0
 48 51  1  0  0  0  0
 22 51  1  0  0  0  0
  1 52  1  0  0  0  0
 52 53  1  0  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
  1 56  1  0  0  0  0
 54 57  2  0  0  0  0
M  END

 
  Mrv1533006051501022D          
 
 57 59  0  0  1  0            999 V2000
   18.5345  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.2490  -19.9650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   19.9634  -20.3775    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
   20.6779  -19.9650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.3924  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.1068  -19.9650    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.8213  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5358  -19.9650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2502  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.9647  -19.9650    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   25.6792  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   26.3936  -19.9650    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   27.1081  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.8226  -19.9650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   28.5370  -20.3775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   19.2490  -19.1401    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.8213  -21.2024    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.6792  -21.2023    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.3936  -19.1400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.1081  -19.5525    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   27.1081  -21.2025    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   29.3620  -20.3775    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   30.1870  -20.3775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.3620  -21.2025    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.5338  -17.4488    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   26.3588  -17.4488    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   26.6137  -16.6641    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   25.9463  -16.1792    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   25.2788  -16.6641    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   27.3913  -16.4114    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   25.0488  -18.1162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   26.8437  -18.1162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.6687  -18.1162    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   27.6687  -17.2912    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   28.4937  -18.1162    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   27.6687  -18.9412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.8525  -15.5925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.8525  -16.4175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   24.2815  -16.4175    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.2815  -15.5925    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   23.5670  -15.1800    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.1381  -15.1800    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.4235  -15.5925    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   21.4235  -16.4175    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.1381  -16.8300    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   22.1381  -14.3551    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   28.5594  -16.6662    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.3844  -16.6662    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   29.3844  -15.8412    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   30.2094  -16.6662    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   29.3844  -18.5637    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.8068  -19.9650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.0923  -20.3775    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.3778  -19.9650    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.6634  -20.3775    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.5377  -21.2023    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.3778  -19.1400    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  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  1  0  0  0  0
  8  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  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
  2 16  2  0  0  0  0
  7 17  2  0  0  0  0
 11 18  2  0  0  0  0
 12 19  1  6  0  0  0
 13 20  1  0  0  0  0
 13 21  1  0  0  0  0
 15 22  1  0  0  0  0
 22 23  2  0  0  0  0
 22 24  1  0  0  0  0
 25 26  1  0  0  0  0
 26 27  1  0  0  0  0
 27 28  1  0  0  0  0
 28 29  1  0  0  0  0
 25 29  1  0  0  0  0
 27 30  1  6  0  0  0
 25 31  1  1  0  0  0
 26 32  1  1  0  0  0
 32 33  1  0  0  0  0
 33 34  1  0  0  0  0
 33 35  1  0  0  0  0
 33 36  2  0  0  0  0
 37 38  2  0  0  0  0
 38 39  1  0  0  0  0
 39 40  1  0  0  0  0
 40 41  2  0  0  0  0
 37 41  1  0  0  0  0
 37 42  1  0  0  0  0
 42 43  2  0  0  0  0
 43 44  1  0  0  0  0
 44 45  2  0  0  0  0
 38 45  1  0  0  0  0
 42 46  1  0  0  0  0
 29 39  1  6  0  0  0
 30 47  1  0  0  0  0
 47 48  1  0  0  0  0
 48 49  1  0  0  0  0
 48 50  2  0  0  0  0
 48 51  1  0  0  0  0
 22 51  1  0  0  0  0
  1 52  1  0  0  0  0
 52 53  1  0  0  0  0
 53 54  1  0  0  0  0
 54 55  1  0  0  0  0
  1 56  1  0  0  0  0
 54 57  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0049880

> <DATABASE_NAME>
MIME

> <SMILES>
CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)C(O)CCC(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)/t13?,14-,18-,19-,20+,24-/m1/s1

> <INCHI_KEY>
ITRSBJZNLOYNNR-RMNRSTNRSA-N

> <FORMULA>
C26H42N7O20P3S

> <MOLECULAR_WEIGHT>
897.63

> <EXACT_MASS>
897.141818948

> <JCHEM_ACCEPTOR_COUNT>
20

> <JCHEM_ATOM_COUNT>
99

> <JCHEM_AVERAGE_POLARIZABILITY>
77.84268596313304

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
11

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
5-[(2-{3-[(2R)-3-[({[({[(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)methyl]-2-hydroxy-3-methylbutanamido]propanamido}ethyl)sulfanyl]-4-hydroxy-5-oxopentanoic acid

> <ALOGPS_LOGP>
-0.76

> <JCHEM_LOGP>
-6.526553561879799

> <ALOGPS_LOGS>
-2.39

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-5

> <JCHEM_PKA>
1.9008079080219864

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8204994323178267

> <JCHEM_PKA_STRONGEST_BASIC>
4.993751069816967

> <JCHEM_POLAR_SURFACE_AREA>
421.15999999999997

> <JCHEM_REFRACTIVITY>
189.19450000000003

> <JCHEM_ROTATABLE_BOND_COUNT>
24

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
3.66e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-hydroxyglutaryl-coa

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JUN-15         0                                  
HETATM    1  C   UNK     0      34.598 -38.038   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      35.931 -37.268   0.000  0.00  0.00           C+0
HETATM    3  S   UNK     0      37.265 -38.038   0.000  0.00  0.00           S+0
HETATM    4  C   UNK     0      38.599 -37.268   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      39.932 -38.038   0.000  0.00  0.00           C+0
HETATM    6  N   UNK     0      41.266 -37.268   0.000  0.00  0.00           N+0
HETATM    7  C   UNK     0      42.600 -38.038   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      43.933 -37.268   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      45.267 -38.038   0.000  0.00  0.00           C+0
HETATM   10  N   UNK     0      46.601 -37.268   0.000  0.00  0.00           N+0
HETATM   11  C   UNK     0      47.934 -38.038   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      49.268 -37.268   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      50.602 -38.038   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      51.936 -37.268   0.000  0.00  0.00           C+0
HETATM   15  O   UNK     0      53.269 -38.038   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      35.931 -35.728   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      42.600 -39.578   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      47.934 -39.578   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0      49.268 -35.728   0.000  0.00  0.00           O+0
HETATM   20  C   UNK     0      50.602 -36.498   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      50.602 -39.578   0.000  0.00  0.00           C+0
HETATM   22  P   UNK     0      54.809 -38.038   0.000  0.00  0.00           P+0
HETATM   23  O   UNK     0      56.349 -38.038   0.000  0.00  0.00           O+0
HETATM   24  O   UNK     0      54.809 -39.578   0.000  0.00  0.00           O+0
HETATM   25  C   UNK     0      47.663 -32.571   0.000  0.00  0.00           C+0
HETATM   26  C   UNK     0      49.203 -32.571   0.000  0.00  0.00           C+0
HETATM   27  C   UNK     0      49.679 -31.106   0.000  0.00  0.00           C+0
HETATM   28  O   UNK     0      48.433 -30.201   0.000  0.00  0.00           O+0
HETATM   29  C   UNK     0      47.187 -31.106   0.000  0.00  0.00           C+0
HETATM   30  C   UNK     0      51.130 -30.635   0.000  0.00  0.00           C+0
HETATM   31  O   UNK     0      46.758 -33.817   0.000  0.00  0.00           O+0
HETATM   32  O   UNK     0      50.108 -33.817   0.000  0.00  0.00           O+0
HETATM   33  P   UNK     0      51.648 -33.817   0.000  0.00  0.00           P+0
HETATM   34  O   UNK     0      51.648 -32.277   0.000  0.00  0.00           O+0
HETATM   35  O   UNK     0      53.188 -33.817   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      51.648 -35.357   0.000  0.00  0.00           O+0
HETATM   37  C   UNK     0      42.658 -29.106   0.000  0.00  0.00           C+0
HETATM   38  C   UNK     0      42.658 -30.646   0.000  0.00  0.00           C+0
HETATM   39  N   UNK     0      45.325 -30.646   0.000  0.00  0.00           N+0
HETATM   40  C   UNK     0      45.325 -29.106   0.000  0.00  0.00           C+0
HETATM   41  N   UNK     0      43.992 -28.336   0.000  0.00  0.00           N+0
HETATM   42  C   UNK     0      41.324 -28.336   0.000  0.00  0.00           C+0
HETATM   43  N   UNK     0      39.991 -29.106   0.000  0.00  0.00           N+0
HETATM   44  C   UNK     0      39.991 -30.646   0.000  0.00  0.00           C+0
HETATM   45  N   UNK     0      41.324 -31.416   0.000  0.00  0.00           N+0
HETATM   46  N   UNK     0      41.324 -26.796   0.000  0.00  0.00           N+0
HETATM   47  O   UNK     0      53.311 -31.110   0.000  0.00  0.00           O+0
HETATM   48  P   UNK     0      54.851 -31.110   0.000  0.00  0.00           P+0
HETATM   49  O   UNK     0      54.851 -29.570   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      56.391 -31.110   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      54.851 -34.652   0.000  0.00  0.00           O+0
HETATM   52  C   UNK     0      33.239 -37.268   0.000  0.00  0.00           C+0
HETATM   53  C   UNK     0      31.906 -38.038   0.000  0.00  0.00           C+0
HETATM   54  C   UNK     0      30.572 -37.268   0.000  0.00  0.00           C+0
HETATM   55  O   UNK     0      29.238 -38.038   0.000  0.00  0.00           O+0
HETATM   56  O   UNK     0      34.604 -39.578   0.000  0.00  0.00           O+0
HETATM   57  O   UNK     0      30.572 -35.728   0.000  0.00  0.00           O+0
CONECT    1    2   52   56                                                  
CONECT    2    1    3   16                                                  
CONECT    3    2    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7                                                       
CONECT    7    6    8   17                                                  
CONECT    8    7    9                                                       
CONECT    9    8   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   18                                                  
CONECT   12   11   13   19                                                  
CONECT   13   12   14   20   21                                             
CONECT   14   13   15                                                       
CONECT   15   14   22                                                       
CONECT   16    2                                                            
CONECT   17    7                                                            
CONECT   18   11                                                            
CONECT   19   12                                                            
CONECT   20   13                                                            
CONECT   21   13                                                            
CONECT   22   15   23   24   51                                             
CONECT   23   22                                                            
CONECT   24   22                                                            
CONECT   25   26   29   31                                                  
CONECT   26   25   27   32                                                  
CONECT   27   26   28   30                                                  
CONECT   28   27   29                                                       
CONECT   29   28   25   39                                                  
CONECT   30   27   47                                                       
CONECT   31   25                                                            
CONECT   32   26   33                                                       
CONECT   33   32   34   35   36                                             
CONECT   34   33                                                            
CONECT   35   33                                                            
CONECT   36   33                                                            
CONECT   37   38   41   42                                                  
CONECT   38   37   39   45                                                  
CONECT   39   38   40   29                                                  
CONECT   40   39   41                                                       
CONECT   41   40   37                                                       
CONECT   42   37   43   46                                                  
CONECT   43   42   44                                                       
CONECT   44   43   45                                                       
CONECT   45   44   38                                                       
CONECT   46   42                                                            
CONECT   47   30   48                                                       
CONECT   48   47   49   50   51                                             
CONECT   49   48                                                            
CONECT   50   48                                                            
CONECT   51   48   22                                                       
CONECT   52    1   53                                                       
CONECT   53   52   54                                                       
CONECT   54   53   55   57                                                  
CONECT   55   54                                                            
CONECT   56    1                                                            
CONECT   57   54                                                            
MASTER        0    0    0    0    0    0    0    0   57    0  118    0
END

Synonyms

Value	Source
2-Hydroxyglutaryl-coenzyme A	ChEBI

Molecular Formula

C₂₆H₄₂N₇O₂₀P₃S

Average Mass

897.63

Monoisotopic Mass

897.141818948

IUPAC Name

5-[(2-{3-[(2R)-3-[({[({[(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)methyl]-2-hydroxy-3-methylbutanamido]propanamido}ethyl)sulfanyl]-4-hydroxy-5-oxopentanoic acid

Traditional Name

2-hydroxyglutaryl-coa

CAS Registry Number

Not Available

SMILES

CC(C)(COP(O)(=O)OP(O)(=O)OC[C@H]1O[C@H]([C@H](O)[C@@H]1OP(O)(O)=O)N1C=NC2=C1N=CN=C2N)[C@@H](O)C(=O)NCCC(=O)NCCSC(=O)C(O)CCC(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)/t13?,14-,18-,19-,20+,24-/m1/s1

InChI Key

ITRSBJZNLOYNNR-RMNRSTNRSA-N

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

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

hydroxyacyl-CoA (CHEBI:28578 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	3.66 g/L	ALOGPS
logP	-0.76	ALOGPS
logP	-6.5	ChemAxon
logS	-2.4	ALOGPS
pKa (Strongest Acidic)	0.82	ChemAxon
pKa (Strongest Basic)	4.99	ChemAxon
Physiological Charge	-5	ChemAxon
Hydrogen Acceptor Count	20	ChemAxon
Hydrogen Donor Count	11	ChemAxon
Polar Surface Area	421.16 Å²	ChemAxon
Rotatable Bond Count	24	ChemAxon
Refractivity	189.19 m³·mol⁻¹	ChemAxon
Polarizability	77.84 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	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-000i-1922000140-d1fc90e6734f473b53b3	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-000i-0934000000-b2c8523d265b7f3e0ea1	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-000i-1911000000-b64bcc864ac0ad13d146	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-017j-3920140750-436de25edbd914cc940d	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-003r-3910110010-e945eb0f39dbd220b724	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-057i-4900100000-a23c2dad2947b1ad4e41	2019-02-23	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	View Spectrum

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	704.7
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	588.2
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	226.2
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	406.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	362.2
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	186.5
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	891.6
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	1013.9
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	383.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	151.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	426.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	173.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	81.0
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	696.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	606.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	78.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	303.0
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	742.7
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	656.1

Retention Indices

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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

Not Available

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
MMDBr0038841	2-Hydroxyglutaryl-CoA	2-Hydroxyglutarate	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	11	Pig ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	17	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	5	Human ; Human feces; Human sputum	Metabolic reconstruction

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
Human Feces	Detected but not Quantified									HMDB

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

Not Available

KEGG Compound ID

C03058

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

11966206

PDB ID

Not Available

ChEBI ID

28578

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for 2-Hydroxyglutaryl-CoA (MMDBc0049880)

MOL for #<Metabolite:0x00007f2e516719a8>

3D MOL for #<Metabolite:0x00007f2e516719a8>

3D SDF for #<Metabolite:0x00007f2e516719a8>

3D-SDF for #<Metabolite:0x00007f2e516719a8>

PDB for #<Metabolite:0x00007f2e516719a8>

3D PDB for #<Metabolite:0x00007f2e516719a8>

SMILES for #<Metabolite:0x00007f2e516719a8>

INCHI for #<Metabolite:0x00007f2e516719a8>

Structure for #<Metabolite:0x00007f2e516719a8>

3D Structure for #<Metabolite:0x00007f2e516719a8>