Showing metabocard for Fumaric acid (MMDBc0000039)

Plant
Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:28:08 UTC
Update Date2022-08-30 23:13:55 UTC
Metabolite IDMMDBc0000039
Metabolite Identification
Common NameFumaric acid
DescriptionFumaric acid is a dicarboxylic acid. It is a precursor to L-malate in the Krebs tricarboxylic acid (TCA) cycle. It is formed by the oxidation of succinic acid by succinate dehydrogenase. Fumarate is converted by the enzyme fumarase to malate. Fumaric acid has recently been identified as an oncometabolite or an endogenous, cancer causing metabolite. High levels of this organic acid can be found in tumors or biofluids surrounding tumors. Its oncogenic action appears to due to its ability to inhibit prolyl hydroxylase-containing enzymes. In many tumours, oxygen availability becomes limited (hypoxia) very quickly due to rapid cell proliferation and limited blood vessel growth. The major regulator of the response to hypoxia is the HIF transcription factor (HIF-alpha). Under normal oxygen levels, protein levels of HIF-alpha are very low due to constant degradation, mediated by a series of post-translational modification events catalyzed by the prolyl hydroxylase domain-containing enzymes PHD1, 2 and 3, (also known as EglN2, 1 and 3) that hydroxylate HIF-alpha and lead to its degradation. All three of the PHD enzymes are inhibited by fumarate. Fumaric acid is found to be associated with fumarase deficiency, which is an inborn error of metabolism. It is also a metabolite of Aspergillus.
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f1240edf798>


  Mrv1652309032023532D          

  8  7  0  0  0  0            999 V2000
   -1.6739   -0.4357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3883   -0.8482    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6739    0.3892    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9594   -0.8482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2449   -0.4357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4694   -0.8482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4694   -1.6732    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1839   -0.4357    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  8  1  0  0  0  0
  6  7  2  0  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f1240edf798>

HMDB0000134
     RDKit          3D
Fumaric acid
 12 11  0  0  0  0  0  0  0  0999 V2000
   -3.0532   -0.7292   -0.3496 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0555    0.0034   -0.1235 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1983    1.3239    0.2276 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7335   -0.5543   -0.2350 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3568    0.1701   -0.0084 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6650   -0.4440   -0.1355 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8084   -1.6463   -0.4547 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7809    0.3180    0.1020 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8700    1.6744    1.1040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5771   -1.6060   -0.5134 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2336    1.1990    0.2648 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6429    0.2909   -0.3982 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  8 12  1  0
M  END
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3D SDF for #<Metabolite:0x00007f1240edf798>


  Mrv1652309032023532D          

  8  7  0  0  0  0            999 V2000
   -1.6739   -0.4357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.3883   -0.8482    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.6739    0.3892    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9594   -0.8482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2449   -0.4357    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4694   -0.8482    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.4694   -1.6732    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.1839   -0.4357    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  4  1  0  0  0  0
  4  5  2  0  0  0  0
  5  6  1  0  0  0  0
  6  8  1  0  0  0  0
  6  7  2  0  0  0  0
  1  3  2  0  0  0  0
  2  1  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000039

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)\C=C\C(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H,5,6)(H,7,8)/b2-1+

> <INCHI_KEY>
VZCYOOQTPOCHFL-OWOJBTEDSA-N

> <FORMULA>
C4H4O4

> <MOLECULAR_WEIGHT>
116.0722

> <EXACT_MASS>
116.010958616

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
12

> <JCHEM_AVERAGE_POLARIZABILITY>
9.352250335599845

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2E)-but-2-enedioic acid

> <ALOGPS_LOGP>
0.21

> <JCHEM_LOGP>
-0.040914331333333324

> <ALOGPS_LOGS>
-0.68

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.412485134930334

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.545732417201611

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
24.607

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.41e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
fumaric acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f1240edf798>

HMDB0000134
     RDKit          3D
Fumaric acid
 12 11  0  0  0  0  0  0  0  0999 V2000
   -3.0532   -0.7292   -0.3496 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0555    0.0034   -0.1235 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1983    1.3239    0.2276 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7335   -0.5543   -0.2350 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3568    0.1701   -0.0084 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.6650   -0.4440   -0.1355 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.8084   -1.6463   -0.4547 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7809    0.3180    0.1020 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.8700    1.6744    1.1040 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5771   -1.6060   -0.5134 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2336    1.1990    0.2648 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.6429    0.2909   -0.3982 H   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  2  0
  2  3  1  0
  2  4  1  0
  4  5  2  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  3  9  1  0
  4 10  1  0
  5 11  1  0
  8 12  1  0
M  END
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PDB for #<Metabolite:0x00007f1240edf798>

HEADER    PROTEIN                                 03-SEP-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   03-SEP-20         0                                  
HETATM    1  C   UNK     0      -3.125  -0.813   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -4.458  -1.583   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      -3.125   0.727   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.791  -1.583   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.457  -0.813   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       0.876  -1.583   0.000  0.00  0.00           C+0
HETATM    7  O   UNK     0       0.876  -3.123   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       2.210  -0.813   0.000  0.00  0.00           O+0
CONECT    1    4    3    2                                                  
CONECT    2    1                                                            
CONECT    3    1                                                            
CONECT    4    1    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    8    7                                                  
CONECT    7    6                                                            
CONECT    8    6                                                            
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for #<Metabolite:0x00007f1240edf798>

COMPND    HMDB0000134
HETATM    1  O1  UNL     1      -3.053  -0.729  -0.350  1.00  0.00           O  
HETATM    2  C1  UNL     1      -2.056   0.003  -0.123  1.00  0.00           C  
HETATM    3  O2  UNL     1      -2.198   1.324   0.228  1.00  0.00           O  
HETATM    4  C2  UNL     1      -0.734  -0.554  -0.235  1.00  0.00           C  
HETATM    5  C3  UNL     1       0.357   0.170  -0.008  1.00  0.00           C  
HETATM    6  C4  UNL     1       1.665  -0.444  -0.135  1.00  0.00           C  
HETATM    7  O3  UNL     1       1.808  -1.646  -0.455  1.00  0.00           O  
HETATM    8  O4  UNL     1       2.781   0.318   0.102  1.00  0.00           O  
HETATM    9  H1  UNL     1      -1.870   1.674   1.104  1.00  0.00           H  
HETATM   10  H2  UNL     1      -0.577  -1.606  -0.513  1.00  0.00           H  
HETATM   11  H3  UNL     1       0.234   1.199   0.265  1.00  0.00           H  
HETATM   12  H4  UNL     1       3.643   0.291  -0.398  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5    5   10
CONECT    5    6   11
CONECT    6    7    7    8
CONECT    8   12
END
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SMILES for #<Metabolite:0x00007f1240edf798>

OC(=O)\C=C\C(O)=O
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INCHI for #<Metabolite:0x00007f1240edf798>

InChI=1S/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H,5,6)(H,7,8)/b2-1+
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Synonyms
ValueSource
(2E)-2-Butenedioic acidChEBI
(e)-2-Butenedioic acidChEBI
e297ChEBI
FumarsaeureChEBI
trans-1,2-Ethylenedicarboxylic acidChEBI
trans-But-2-enedioic acidChEBI
trans-Butenedioic acidChEBI
(2E)-2-ButenedioateGenerator
(e)-2-ButenedioateGenerator
trans-1,2-EthylenedicarboxylateGenerator
trans-But-2-enedioateGenerator
trans-ButenedioateGenerator
FumarateGenerator
(2E)-But-2-enedioateHMDB
(2E)-But-2-enedioic acidHMDB
2-(e)-ButenedioateHMDB
2-(e)-Butenedioic acidHMDB
AllomaleateHMDB
Allomaleic acidHMDB
BoletateHMDB
Boletic acidHMDB
FC 33HMDB
LichenateHMDB
Lichenic acidHMDB
trans-2-ButenedioateHMDB
trans-2-Butenedioic acidHMDB
FuramagHMDB
MafusolHMDB
Fumaric acidHMDB
Molecular FormulaC4H4O4
Average Mass116.0722
Monoisotopic Mass116.010958616
IUPAC Name(2E)-but-2-enedioic acid
Traditional Namefumaric acid
CAS Registry Number110-17-8
SMILES
OC(=O)\C=C\C(O)=O
InChI Identifier
InChI=1S/C4H4O4/c5-3(6)1-2-4(7)8/h1-2H,(H,5,6)(H,7,8)/b2-1+
InChI KeyVZCYOOQTPOCHFL-OWOJBTEDSA-N