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Methylmalonyl-CoA

Athanor · official

C25H40N7O19P3S · 867.6 g/mol

IUPAC name: (2S)-3-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-2-hydroxy-3,3-dimethylbutanoyl]amino]propanoylamino]ethylsulfanyl]-2-methyl-3-oxopropanoic acid

Also called B12 pathway, propionate metabolism, methylmalonyl coenzyme A

MetabolitesNucleic acid parts
Open in Athanor
The structure of Methylmalonyl-CoA
Drawn from its SMILES with RDKit
Harmful or irritantWarningCauses skin irritation · Causes serious eye irritation · May cause respiratory irritation

Names and identifiers

IUPAC name
(2S)-3-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-2-hydroxy-3,3-dimethylbutanoyl]amino]propanoylamino]ethylsulfanyl]-2-methyl-3-oxopropanoic acid
Synonyms
B12 pathway, propionate metabolism, methylmalonyl coenzyme A
+ 24 more

(S)-Methylmalonyl-CoA, (2S)-Methylmalonyl-CoA, D-methylmalonyl-CoA, CHEBI:15466, (S)-2-Methyl-3-oxopropanoyl-CoA, (S)-2-Methyl-3-oxopropionyl-CoA, (S)-3-oxo-2-methylpropanoyl-CoA, 3'-phosphoadenosine 5'-{3-[(3R)-3-hydroxy-2,2-dimethyl-4-({3-[(2-{[(2S)-2-methyl-3-oxopropanoyl]sulfanyl}ethyl)amino]-3-oxopropyl}amino)-4-oxobutyl] dihydrogen diphosphate}, (2S)-3-[2-[3-[[(2R)-4-[[[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-yl]methoxy-hydroxyphosphoryl]oxy-hydroxyphosphoryl]oxy-2-hydroxy-3,3-dimethylbutanoyl]amino]propanoylamino]ethylsulfanyl]-2-methyl-3-oxopropanoic acid, (2S)-methyl-malonyl-CoA, S-Methylmalonyl-CoA, (2S)-3-((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)-1,2-dihydroxy-3,3-dimethylbutylidene)amino)-1-hydroxypropylidene)amino)ethyl)sulfanyl)-2-methyl-3-oxopropanoic acid, (2S)-3-({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)-1,2-dihydroxy-3,3-dimethylbutylidene]amino}-1-hydroxypropylidene)amino]ethyl}sulfanyl)-2-methyl-3-oxopropanoic acid, (2S)-3-(2-(3-(((2R)-4-((((2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-4-hydroxy-3-phosphonooxyoxolan-2-yl)methoxy-hydroxyphosphoryl)oxy-hydroxyphosphoryl)oxy-2-hydroxy-3,3-dimethylbutanoyl)amino)propanoylamino)ethylsulfanyl)-2-methyl-3-oxopropanoic acid, 3'-phosphoadenosine 5'-(3-((3R)-3-hydroxy-2,2-dimethyl-4-((3-((2-(((2S)-2-methyl-3-oxopropanoyl)sulfanyl)ethyl)amino)-3-oxopropyl)amino)-4-oxobutyl) dihydrogen diphosphate), RefChem:70496, (S)-Methylmalonyl-coenzyme A, SCHEMBL188315, SCHEMBL30074506, LMFA07050164, C00683, Q27089452, (3S,5R,9R,20S)-1-[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-4-hydroxy-3-(phosphonooxy)tetrahydrofuran-2-yl]-3,5,9-trihydroxy-8,8,20-trimethyl-10,14,19-trioxo-2,4,6-trioxa-18-thia-11,15-diaza-3,5-diphosphahenicosan-21-oic acid 3,5-dioxide (non-preferred name), MC0

Molecular formula
C25H40N7O19P3S
Empirical formula
C25H40N7O19P3S
Molecular weight
867.6 g/mol
Exact mass
867.13125
CAS number
1264-45-5
PubChem CID
11966111
Canonical SMILES
CC(C(=O)O)C(=O)SCCNC(=O)CCNC(=O)C(C(C)(C)COP(=O)(O)OP(=O)(O)OCC1C(C(C(O1)N2C=NC3=C(N=CN=C32)N)O)OP(=O)(O)O)O
Isomeric SMILES
C[C@@H](C(=O)O)C(=O)SCCNC(=O)CCNC(=O)[C@@H](C(C)(C)COP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)N2C=NC3=C(N=CN=C32)N)O)OP(=O)(O)O)O
InChI
InChI=1S/C25H40N7O19P3S/c1-12(23(37)38)24(39)55-7-6-27-14(33)4-5-28-21(36)18(35)25(2,3)9-48-54(45,46)51-53(43,44)47-8-13-17(50-52(40,41)42)16(34)22(49-13)32-11-31-15-19(26)29-10-30-20(15)32/h10-13,16-18,22,34-35H,4-9H2,1-3H3,(H,27,33)(H,28,36)(H,37,38)(H,43,44)(H,45,46)(H2,26,29,30)(H2,40,41,42)/t12-,13+,16+,17+,18-,22+/m0/s1
InChIKey
MZFOKIKEPGUZEN-IBNUZSNCSA-N
Molfile

Names, InChI and the identifiers from PubChem, retrieved 2026-10-14.

Calculated

Heavy atoms
55
Rings
3
Aromatic rings
2
Fraction sp³ carbons (Fsp3)
0.64
H-bond donors
10
H-bond acceptors
19 computed here · PubChem 24
Rotatable bonds
21 computed here · PubChem 22
TPSA (Ų)
400.9 computed here · PubChem 426
Formal charge
0
XLogP3
-5.4 PubChem
Complexity
1530 PubChem
Stereocenters
6 defined, 2 undefinedCIP: C2: S · C19: R · P26: undefined · P30: undefined · C35: R · C37: R · C48: R · C50: S
Double-bond geometry
None specified
Point group
C1 of one 3D conformer with its hydrogens, by Athanor’s engine (as in the app)

Elemental analysis

  • C34.61%
  • H4.65%
  • N11.30%
  • O35.04%
  • P10.71%
  • S3.70%

Isotope pattern

100%867.13132%868.13413%869.1333.1%870.135871.136872.137

Each peak is a nominal mass with its abundance-weighted exact mass, as a percentage of the tallest, from IUPAC natural isotope abundances.

Computed from the structure with RDKit 2026.09 when this page was built, beside PubChem's own computed values from its record; where the two differ, both are shown.

Predicted

log P
-1.61 Crippen (Wildman and Crippen 1999)
log S (water solubility)
-2.94 ESOL (Delaney 2004), log mol/L
Synthetic accessibility
5.33 SA score, 1 easy to 10 hard (Ertl and Schuffenhauer 2009)

Drug-likeness: Lipinski’s rule of five

  • Molecular weight ≤ 500: 867.61
  • log P ≤ 5 (Crippen): -1.61
  • H-bond donors ≤ 5: 10
  • H-bond acceptors ≤ 10: 19

Breaks 3 of the four rules.

¹³C NMR shifts, predicted

Predictions, not measurements; each names its method. A measured log P, where a source reports one, is under Physical properties.

Safety

Warning

Most widely reported: 39 company reports to ECHA. Source [1].

  • Harmful or irritant
  • H315Causes skin irritation
  • H319Causes serious eye irritation
  • H335May cause respiratory irritation

Precautionary statements: P261, P264, P264+P265, P271, P280, P302+P352, P304+P340, P305+P351+P338, P319, P321, P332+P317, P337+P317, P362+P364, P403+P233, P405, P501

Safety data sheets on the supplier’s page: BenchChem, J&H Chemical Co.,ltd, eNovation Chemicals.

Always read the supplier’s safety data sheet before working with it.

Literature

Reading PubChem, OpenAlex and GSRS…

Bioactivity

Reading ChEMBL…

References

  1. [1]European Chemicals Agency (ECHA) · ECHA legal notice: reuse with acknowledgement · via PubChem · retrieved 2026-10-14
  2. ·Calculated values: computed by Athanor with RDKit 2026.09 from the structure.
  3. ·Literature on PubChem

Data last updated 2026-10-14.