MiMeDB: Showing metabocard for (S)-malyl-CoA (MMDBc0055071)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:41:17 UTC

Update Date

2025-10-07 16:08:54 UTC

Metabolite ID

MMDBc0055071

Metabolite Identification

Common Name

(S)-malyl-CoA

Description

(S)-malyl-CoA is a member of the acyl-CoA chemical class, specifically a malyl-CoA derivative involved in various metabolic pathways. Chemically, it is formed from acetyl-CoA and two molecules of bicarbonate during the first cycle of the malyl-CoA pathway (PMID:19955419 ). The structure of (S)-malyl-CoA allows for its cleavage, which releases glyoxylate, a product of CO(2) fixation, and regenerates acetyl-CoA, thus participating in carbon fixation processes (PMID:19955419 ). Additionally, (S)-malyl-CoA plays a role in the conversion to (S)-citramalyl-CoA, which is subsequently cleaved into acetyl-CoA and pyruvate by a tri-functional lyase; this enzyme also acts on (S)-malyl-CoA to form beta-methylmalyl-CoA (PMID:19955419 ). Overall, (S)-malyl-CoA is integral to metabolic pathways involving carbon fixation and the interconversion of key metabolic intermediates.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221412D          

 62 64  0  0  1  0            999 V2000
    0.7578   19.2703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4078   19.2703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0117   15.9703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0117   16.7953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4406   14.3203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1551   14.7328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2985   14.3203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5607   23.8078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5828   20.0953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5345   26.3301    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8138   23.6971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0130   14.7328    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2751   24.2203    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7262   15.5578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5841   14.7328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7070   24.6891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1683   25.2123    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3614   25.0407    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5828   18.4453    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.3745   25.1740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9533   25.0247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2972   18.0328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5808   24.4978    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.7275   14.3203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5828   19.2703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1281   24.8385    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7262   14.7328    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2972   17.2078    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2882   25.9945    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8671   25.8451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6208   23.8686    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4013   24.4116    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.0130   15.5578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4406   15.9703    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.5841   15.5578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5039   25.9659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8683   18.0328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0117   18.4453    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    9.4419   14.7328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7275   13.4953    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.2186   24.5532    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.2913   26.1225    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.8210   25.0829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2587   21.8558    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5663   23.2847    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0433   21.3328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6933   21.3328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5607   22.9828    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8683   20.5078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0288   23.8847    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7483   25.5928    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8683   22.1578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0364   25.3378    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.1538   22.5703    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.8683   21.3328    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.8696   14.3203    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    8.0130   13.9078    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5832   24.6696    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6491   25.8534    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9745   24.4887    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2972   18.8578    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0302   25.1897    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
 12  7  1  0  0  0  0
 13  8  1  1  0  0  0
 14  3  1  0  0  0  0
 15  7  1  0  0  0  0
 18 13  1  0  0  0  0
 18 17  1  0  0  0  0
 20 16  2  0  0  0  0
 21 16  1  0  0  0  0
 22 19  1  0  0  0  0
 23 17  1  0  0  0  0
 24 12  1  0  0  0  0
 25  1  1  0  0  0  0
 25  2  1  0  0  0  0
 25  9  1  0  0  0  0
 25 19  1  0  0  0  0
 26 20  1  0  0  0  0
 27  5  1  4  0  0  0
 27 14  2  0  0  0  0
 28  4  1  4  0  0  0
 28 22  2  0  0  0  0
 29 10  2  0  0  0  0
 29 20  1  0  0  0  0
 30 10  1  0  0  0  0
 30 21  2  0  0  0  0
 31 11  2  0  0  0  0
 31 16  1  0  0  0  0
 32 11  1  0  0  0  0
 32 21  1  0  0  0  0
 23 32  1  1  0  0  0
 12 33  1  1  0  0  0
 34 14  1  0  0  0  0
 35 15  2  0  0  0  0
 17 36  1  6  0  0  0
 19 37  1  1  0  0  0
 38 22  1  0  0  0  0
 39 24  2  0  0  0  0
 40 24  1  0  0  0  0
 48  8  1  0  0  0  0
 49  9  1  0  0  0  0
 50 13  1  0  0  0  0
 50 23  1  0  0  0  0
 18 51  1  1  0  0  0
 53 41  1  0  0  0  0
 53 42  1  0  0  0  0
 53 43  2  0  0  0  0
 53 51  1  0  0  0  0
 54 44  1  0  0  0  0
 54 45  2  0  0  0  0
 54 48  1  0  0  0  0
 54 52  1  0  0  0  0
 55 46  1  0  0  0  0
 55 47  2  0  0  0  0
 55 49  1  0  0  0  0
 55 52  1  0  0  0  0
 56  6  1  0  0  0  0
 56 15  1  0  0  0  0
 12 57  1  1  0  0  0
 13 58  1  6  0  0  0
 17 59  1  1  0  0  0
 18 60  1  1  0  0  0
 19 61  1  1  0  0  0
 23 62  1  6  0  0  0
M  CHG  5  34  -1  38  -1  40  -1  41  -1  42  -1
M  END


  Mrv1652306172221412D          

 62 64  0  0  1  0            999 V2000
    0.7578   19.2703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4078   19.2703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0117   15.9703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.0117   16.7953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.4406   14.3203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.1551   14.7328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    7.2985   14.3203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5607   23.8078    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5828   20.0953    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.5345   26.3301    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8138   23.6971    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    8.0130   14.7328    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -1.2751   24.2203    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    3.7262   15.5578    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    6.5841   14.7328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -4.7070   24.6891    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1683   25.2123    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.3614   25.0407    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.5828   18.4453    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -5.3745   25.1740    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -3.9533   25.0247    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.2972   18.0328    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5808   24.4978    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    8.7275   14.3203    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.5828   19.2703    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -6.1281   24.8385    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    3.7262   14.7328    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    2.2972   17.2078    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -5.2882   25.9945    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.8671   25.8451    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -4.6208   23.8686    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   -3.4013   24.4116    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
    8.0130   15.5578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.4406   15.9703    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.5841   15.5578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.5039   25.9659    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8683   18.0328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.0117   18.4453    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    9.4419   14.7328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.7275   13.4953    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.2186   24.5532    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.2913   26.1225    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.8210   25.0829    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2587   21.8558    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5663   23.2847    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0433   21.3328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6933   21.3328    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5607   22.9828    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8683   20.5078    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0288   23.8847    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7483   25.5928    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8683   22.1578    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0364   25.3378    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.1538   22.5703    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.8683   21.3328    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.8696   14.3203    0.0000 S   0  0  0  0  0  0  0  0  0  0  0  0
    8.0130   13.9078    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5832   24.6696    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6491   25.8534    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.9745   24.4887    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2972   18.8578    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -3.0302   25.1897    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
 12  7  1  0  0  0  0
 13  8  1  1  0  0  0
 14  3  1  0  0  0  0
 15  7  1  0  0  0  0
 18 13  1  0  0  0  0
 18 17  1  0  0  0  0
 20 16  2  0  0  0  0
 21 16  1  0  0  0  0
 22 19  1  0  0  0  0
 23 17  1  0  0  0  0
 24 12  1  0  0  0  0
 25  1  1  0  0  0  0
 25  2  1  0  0  0  0
 25  9  1  0  0  0  0
 25 19  1  0  0  0  0
 26 20  1  0  0  0  0
 27  5  1  4  0  0  0
 27 14  2  0  0  0  0
 28  4  1  4  0  0  0
 28 22  2  0  0  0  0
 29 10  2  0  0  0  0
 29 20  1  0  0  0  0
 30 10  1  0  0  0  0
 30 21  2  0  0  0  0
 31 11  2  0  0  0  0
 31 16  1  0  0  0  0
 32 11  1  0  0  0  0
 32 21  1  0  0  0  0
 23 32  1  1  0  0  0
 12 33  1  1  0  0  0
 34 14  1  0  0  0  0
 35 15  2  0  0  0  0
 17 36  1  6  0  0  0
 19 37  1  1  0  0  0
 38 22  1  0  0  0  0
 39 24  2  0  0  0  0
 40 24  1  0  0  0  0
 48  8  1  0  0  0  0
 49  9  1  0  0  0  0
 50 13  1  0  0  0  0
 50 23  1  0  0  0  0
 18 51  1  1  0  0  0
 53 41  1  0  0  0  0
 53 42  1  0  0  0  0
 53 43  2  0  0  0  0
 53 51  1  0  0  0  0
 54 44  1  0  0  0  0
 54 45  2  0  0  0  0
 54 48  1  0  0  0  0
 54 52  1  0  0  0  0
 55 46  1  0  0  0  0
 55 47  2  0  0  0  0
 55 49  1  0  0  0  0
 55 52  1  0  0  0  0
 56  6  1  0  0  0  0
 56 15  1  0  0  0  0
 12 57  1  1  0  0  0
 13 58  1  6  0  0  0
 17 59  1  1  0  0  0
 18 60  1  1  0  0  0
 19 61  1  1  0  0  0
 23 62  1  6  0  0  0
M  CHG  5  34  -1  38  -1  40  -1  41  -1  42  -1
M  END
> <DATABASE_ID>
MMDBc0055071

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@](O)(CC(=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)C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C25H40N7O20P3S/c1-25(2,19(37)22(38)28-4-3-14(34)27-5-6-56-15(35)7-12(33)24(39)40)9-49-55(46,47)52-54(44,45)48-8-13-18(51-53(41,42)43)17(36)23(50-13)32-11-31-16-20(26)29-10-30-21(16)32/h10-13,17-19,23,33,36-37H,3-9H2,1-2H3,(H,27,34)(H,28,38)(H,39,40)(H,44,45)(H,46,47)(H2,26,29,30)(H2,41,42,43)/p-5/t12-,13+,17+,18+,19-,23+/m0/s1

> <INCHI_KEY>
HJQWLHMLMCDAEL-ZTGLTYRUSA-I

> <FORMULA>
C25H35N7O20P3S

> <MOLECULAR_WEIGHT>
878.57

> <EXACT_MASS>
878.089786623

> <JCHEM_ACCEPTOR_COUNT>
22

> <JCHEM_ATOM_COUNT>
91

> <JCHEM_AVERAGE_POLARIZABILITY>
75.47434494383933

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
-5

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2S)-4-({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)-2-hydroxy-4-oxobutanoate

> <JCHEM_LOGP>
-5.138640068737232

> <JCHEM_MDDR_LIKE_RULE>
1

> <JCHEM_NUMBER_OF_RINGS>
3

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-5

> <JCHEM_PKA>
1.8727282876912006

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8178504343625197

> <JCHEM_PKA_STRONGEST_BASIC>
4.201120824885777

> <JCHEM_POLAR_SURFACE_AREA>
442.2900000000001

> <JCHEM_REFRACTIVITY>
215.17720000000008

> <JCHEM_ROTATABLE_BOND_COUNT>
23

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
(2S)-4-({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)-2-hydroxy-4-oxobutanoate

> <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       1.414  35.971   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       4.494  35.971   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       5.622  29.811   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       5.622  31.351   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       8.289  26.731   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       9.623  27.501   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      13.624  26.731   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      -1.047  44.441   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       2.954  37.511   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0      -8.464  49.149   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0      -7.119  44.235   0.000  0.00  0.00           C+0
HETATM   12  C   UNK     0      14.958  27.501   0.000  0.00  0.00           C+0
HETATM   13  C   UNK     0      -2.380  45.211   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0       6.956  29.041   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      12.290  27.501   0.000  0.00  0.00           C+0
HETATM   16  C   UNK     0      -8.786  46.086   0.000  0.00  0.00           C+0
HETATM   17  C   UNK     0      -4.048  47.063   0.000  0.00  0.00           C+0
HETATM   18  C   UNK     0      -2.541  46.743   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0       2.954  34.431   0.000  0.00  0.00           C+0
HETATM   20  C   UNK     0     -10.032  46.992   0.000  0.00  0.00           C+0
HETATM   21  C   UNK     0      -7.380  46.713   0.000  0.00  0.00           C+0
HETATM   22  C   UNK     0       4.288  33.661   0.000  0.00  0.00           C+0
HETATM   23  C   UNK     0      -4.818  45.729   0.000  0.00  0.00           C+0
HETATM   24  C   UNK     0      16.291  26.731   0.000  0.00  0.00           C+0
HETATM   25  C   UNK     0       2.954  35.971   0.000  0.00  0.00           C+0
HETATM   26  N   UNK     0     -11.439  46.365   0.000  0.00  0.00           N+0
HETATM   27  N   UNK     0       6.956  27.501   0.000  0.00  0.00           N+0
HETATM   28  N   UNK     0       4.288  32.121   0.000  0.00  0.00           N+0
HETATM   29  N   UNK     0      -9.871  48.523   0.000  0.00  0.00           N+0
HETATM   30  N   UNK     0      -7.219  48.244   0.000  0.00  0.00           N+0
HETATM   31  N   UNK     0      -8.625  44.555   0.000  0.00  0.00           N+0
HETATM   32  N   UNK     0      -6.349  45.568   0.000  0.00  0.00           N+0
HETATM   33  O   UNK     0      14.958  29.041   0.000  0.00  0.00           O+0
HETATM   34  O   UNK     0       8.289  29.811   0.000  0.00  0.00           O-1
HETATM   35  O   UNK     0      12.290  29.041   0.000  0.00  0.00           O+0
HETATM   36  O   UNK     0      -4.674  48.470   0.000  0.00  0.00           O+0
HETATM   37  O   UNK     0       1.621  33.661   0.000  0.00  0.00           O+0
HETATM   38  O   UNK     0       5.622  34.431   0.000  0.00  0.00           O-1
HETATM   39  O   UNK     0      17.625  27.501   0.000  0.00  0.00           O+0
HETATM   40  O   UNK     0      16.291  25.191   0.000  0.00  0.00           O-1
HETATM   41  O   UNK     0      -0.408  45.833   0.000  0.00  0.00           O-1
HETATM   42  O   UNK     0       0.544  48.762   0.000  0.00  0.00           O-1
HETATM   43  O   UNK     0       1.532  46.821   0.000  0.00  0.00           O+0
HETATM   44  O   UNK     0      -0.483  40.797   0.000  0.00  0.00           O+0
HETATM   45  O   UNK     0       1.057  43.465   0.000  0.00  0.00           O+0
HETATM   46  O   UNK     0       0.081  39.821   0.000  0.00  0.00           O+0
HETATM   47  O   UNK     0       3.161  39.821   0.000  0.00  0.00           O+0
HETATM   48  O   UNK     0      -1.047  42.901   0.000  0.00  0.00           O+0
HETATM   49  O   UNK     0       1.621  38.281   0.000  0.00  0.00           O+0
HETATM   50  O   UNK     0      -3.787  44.585   0.000  0.00  0.00           O+0
HETATM   51  O   UNK     0      -1.397  47.773   0.000  0.00  0.00           O+0
HETATM   52  O   UNK     0       1.621  41.361   0.000  0.00  0.00           O+0
HETATM   53  P   UNK     0       0.068  47.297   0.000  0.00  0.00           P+0
HETATM   54  P   UNK     0       0.287  42.131   0.000  0.00  0.00           P+0
HETATM   55  P   UNK     0       1.621  39.821   0.000  0.00  0.00           P+0
HETATM   56  S   UNK     0      10.957  26.731   0.000  0.00  0.00           S+0
HETATM   57  H   UNK     0      14.958  25.961   0.000  0.00  0.00           H+0
HETATM   58  H   UNK     0      -1.089  46.050   0.000  0.00  0.00           H+0
HETATM   59  H   UNK     0      -3.078  48.260   0.000  0.00  0.00           H+0
HETATM   60  H   UNK     0      -3.686  45.712   0.000  0.00  0.00           H+0
HETATM   61  H   UNK     0       4.288  35.201   0.000  0.00  0.00           H+0
HETATM   62  H   UNK     0      -5.656  47.021   0.000  0.00  0.00           H+0
CONECT    1   25                                                            
CONECT    2   25                                                            
CONECT    3    4   14                                                       
CONECT    4    3   28                                                       
CONECT    5    6   27                                                       
CONECT    6    5   56                                                       
CONECT    7   12   15                                                       
CONECT    8   13   48                                                       
CONECT    9   25   49                                                       
CONECT   10   29   30                                                       
CONECT   11   31   32                                                       
CONECT   12    7   24   33   57                                             
CONECT   13    8   18   50   58                                             
CONECT   14    3   27   34                                                  
CONECT   15    7   35   56                                                  
CONECT   16   20   21   31                                                  
CONECT   17   18   23   36   59                                             
CONECT   18   13   17   51   60                                             
CONECT   19   22   25   37   61                                             
CONECT   20   16   26   29                                                  
CONECT   21   16   30   32                                                  
CONECT   22   19   28   38                                                  
CONECT   23   17   32   50   62                                             
CONECT   24   12   39   40                                                  
CONECT   25    1    2    9   19                                             
CONECT   26   20                                                            
CONECT   27    5   14                                                       
CONECT   28    4   22                                                       
CONECT   29   10   20                                                       
CONECT   30   10   21                                                       
CONECT   31   11   16                                                       
CONECT   32   11   21   23                                                  
CONECT   33   12                                                            
CONECT   34   14                                                            
CONECT   35   15                                                            
CONECT   36   17                                                            
CONECT   37   19                                                            
CONECT   38   22                                                            
CONECT   39   24                                                            
CONECT   40   24                                                            
CONECT   41   53                                                            
CONECT   42   53                                                            
CONECT   43   53                                                            
CONECT   44   54                                                            
CONECT   45   54                                                            
CONECT   46   55                                                            
CONECT   47   55                                                            
CONECT   48    8   54                                                       
CONECT   49    9   55                                                       
CONECT   50   13   23                                                       
CONECT   51   18   53                                                       
CONECT   52   54   55                                                       
CONECT   53   41   42   43   51                                             
CONECT   54   44   45   48   52                                             
CONECT   55   46   47   49   52                                             
CONECT   56    6   15                                                       
CONECT   57   12                                                            
CONECT   58   13                                                            
CONECT   59   17                                                            
CONECT   60   18                                                            
CONECT   61   19                                                            
CONECT   62   23                                                            
MASTER        0    0    0    0    0    0    0    0   62    0  128    0
END

Synonyms

Value	Source
(3S)-3-Carboxy-3-hydroxypropanoyl-CoA pentaanion	ChEBI
(3S)-3-Carboxy-3-hydroxypropanoyl-coenzyme A(5-)	ChEBI

Molecular Formula

C₂₅H₃₅N₇O₂₀P₃S

Average Mass

878.57

Monoisotopic Mass

878.089786623

IUPAC Name

(2S)-4-({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)-2-hydroxy-4-oxobutanoate

Traditional Name

(2S)-4-({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)-2-hydroxy-4-oxobutanoate

CAS Registry Number

Not Available

SMILES

[H][C@](O)(CC(=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)C([O-])=O

InChI Identifier

InChI=1S/C25H40N7O20P3S/c1-25(2,19(37)22(38)28-4-3-14(34)27-5-6-56-15(35)7-12(33)24(39)40)9-49-55(46,47)52-54(44,45)48-8-13-18(51-53(41,42)43)17(36)23(50-13)32-11-31-16-20(26)29-10-30-21(16)32/h10-13,17-19,23,33,36-37H,3-9H2,1-2H3,(H,27,34)(H,28,38)(H,39,40)(H,44,45)(H,46,47)(H2,26,29,30)(H2,41,42,43)/p-5/t12-,13+,17+,18+,19-,23+/m0/s1

InChI Key

HJQWLHMLMCDAEL-ZTGLTYRUSA-I

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as (r)-3-hydroxyacyl coas. These are organic compounds containing a (R)-3-hydroxyl acylated coenzyme A derivative.

Kingdom

Organic compounds

Super Class

Lipids and lipid-like molecules

Class

Fatty Acyls

Sub Class

Fatty acyl thioesters

Direct Parent

(R)-3-hydroxyacyl CoAs

Alternative Parents

Substituents

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

Molecular Framework

Aromatic heteropolycyclic compounds

External Descriptors

monocarboxylic acid anion (CHEBI:57317 )
acyl-CoA oxoanion (CHEBI:57317 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-5.1	ChemAxon
pKa (Strongest Acidic)	0.82	ChemAxon
pKa (Strongest Basic)	4.2	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	23	ChemAxon
Refractivity	215.18 m³·mol⁻¹	ChemAxon
Polarizability	75.47 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

Not Available

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 (void)	2025-10-24	593.1
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	437.7
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	349.2
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	447.8
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	340.4
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (eluted)	2025-10-24	171.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	1451.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	530.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	389.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	143.4
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	222.4
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	158.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	100.2
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	480.1
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	368.1
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	85.0
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	221.8
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	909.6
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	682.3

Retention Indices

Not Available

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

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
MMDBr0038886	(S)-malyl-CoA	(S)-malate(2-)	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
Archaea/Archaea	Euryarchaeota	1
Bacteria/Eubacteria	Proteobacteria	8	Human ; Human feces
Bacteria/Eubacteria	Chloroflexi	2

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

26330695

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

45266554

PDB ID

Not Available

ChEBI ID

57317

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 (S)-malyl-CoA (MMDBc0055071)

MOL for #<Metabolite:0x0000564323107ec8>

3D MOL for #<Metabolite:0x0000564323107ec8>

3D SDF for #<Metabolite:0x0000564323107ec8>

3D-SDF for #<Metabolite:0x0000564323107ec8>

PDB for #<Metabolite:0x0000564323107ec8>

3D PDB for #<Metabolite:0x0000564323107ec8>

SMILES for #<Metabolite:0x0000564323107ec8>

INCHI for #<Metabolite:0x0000564323107ec8>

Structure for #<Metabolite:0x0000564323107ec8>

3D Structure for #<Metabolite:0x0000564323107ec8>