Showing metabocard for Succinic acid (MMDBc0000087)

Record Information
Version1.0
StatusDetected and Quantified
Creation Date2020-10-27 23:29:54 UTC
Update Date2022-08-30 23:33:45 UTC
Metabolite IDMMDBc0000087
Metabolite Identification
Common NameSuccinic acid
DescriptionSuccinic acid is a dicarboxylic acid. The anion, succinate, is a component of the citric acid or TCA cycle and is capable of donating electrons to the electron transfer chain. Succinate dehydrogenase (SDH) plays an important role in mitochondrial function, being both part of the respiratory chain and the Krebs cycle. SDH with a covalently attached FAD prosthetic group, is able to bind several different enzyme substrates (succinate and fumarate) and physiological regulators (oxaloacetate and ATP). Oxidizing succinate links SDH to the fast-cycling Krebs cycle portion where it participates in the breakdown of acetyl-CoA throughout the entire Krebs cycle. Succinate can readily be imported into the mitochondrial matrix by the n-butylmalonate- (or phenylsuccinate-) sensitive dicarboxylate carrier in exchange with inorganic phosphate or another organic acid, e. g. malate (PMID 16143825 ). Mutations in the four genes encoding the subunits of the mitochondrial succinate dehydrogenase are associated with a wide spectrum of clinical presentations, i.e.: Huntington's disease (PMID 11803021 ). Moreover, succinic acid is found to be associated with D-2-hydroxyglutaric aciduria, which is an inborn error of metabolism. Succinic 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 succinate. Succinic acid is found to be associated with D-2-hydroxyglutaric aciduria, which is an inborn error of metabolism. Succinic acid is also a microbial metabolite, urinary succinic acid is produced by Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumonia, Enterobacter, Acinetobacter, Proteus mirabilis, Citrobacter frundii, Enterococcus faecalis (PMID: 22292465 ). Succinic acid is also found in Actinobacillus, Anaerobiospirillum, Mannheimia, Corynebacterium and Basfia (PMID: 22292465 ; PMID: 18191255 ; PMID: 26360870 ).
Structure
MOL3D MOLSDF3D SDFPDB3D PDBSMILESInChI

MOL for #<Metabolite:0x00007f5a9c47ddc8>


  Mrv1652309032023582D          

  8  7  0  0  0  0            999 V2000
    2.0928    0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6650   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8072   -1.0311    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9504    1.0311    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5217    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2361   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8072   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9504    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  7  2  0  0  0  0
  4  8  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
M  END
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3D MOL for #<Metabolite:0x00007f5a9c47ddc8>

HMDB0000254
     RDKit          3D
Succinic acid
 14 13  0  0  0  0  0  0  0  0999 V2000
    2.8686    0.7889   -0.7361 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9035    0.2266   -0.1638 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1747   -0.4955    0.9882 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5430    0.3600   -0.7380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -0.4191    0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7892   -0.3809   -0.2775 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1591   -1.0952   -1.2456 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7536    0.4134    0.3186 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6648   -0.2075    1.8241 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4587   -0.0937   -1.7508 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2383    1.4201   -0.8463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0116   -1.4669    0.1728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2699   -0.0395    1.1987 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4699    0.9892    1.0923 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  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  8 14  1  0
M  END
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3D SDF for #<Metabolite:0x00007f5a9c47ddc8>


  Mrv1652309032023582D          

  8  7  0  0  0  0            999 V2000
    2.0928    0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6650   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8072   -1.0311    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9504    1.0311    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5217    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2361   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8072   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9504    0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
  1  7  1  0  0  0  0
  2  8  1  0  0  0  0
  3  7  2  0  0  0  0
  4  8  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  6  8  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0000087

> <DATABASE_NAME>
MIME

> <SMILES>
OC(=O)CCC(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C4H6O4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)(H,7,8)

> <INCHI_KEY>
KDYFGRWQOYBRFD-UHFFFAOYSA-N

> <FORMULA>
C4H6O4

> <MOLECULAR_WEIGHT>
118.088

> <EXACT_MASS>
118.02660868

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_ATOM_COUNT>
14

> <JCHEM_AVERAGE_POLARIZABILITY>
10.141334051490146

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
butanedioic acid

> <ALOGPS_LOGP>
-0.53

> <JCHEM_LOGP>
-0.3984829673333332

> <ALOGPS_LOGS>
0.25

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
5.6869121792916

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.5541665109763474

> <JCHEM_POLAR_SURFACE_AREA>
74.6

> <JCHEM_REFRACTIVITY>
23.537

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.11e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
succinic acid

> <JCHEM_VEBER_RULE>
0

$$$$
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3D-SDF for #<Metabolite:0x00007f5a9c47ddc8>

HMDB0000254
     RDKit          3D
Succinic acid
 14 13  0  0  0  0  0  0  0  0999 V2000
    2.8686    0.7889   -0.7361 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9035    0.2266   -0.1638 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1747   -0.4955    0.9882 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5430    0.3600   -0.7380 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3984   -0.4191    0.1635 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7892   -0.3809   -0.2775 C   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1591   -1.0952   -1.2456 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.7536    0.4134    0.3186 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6648   -0.2075    1.8241 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.4587   -0.0937   -1.7508 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.2383    1.4201   -0.8463 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0116   -1.4669    0.1728 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.2699   -0.0395    1.1987 H   0  0  0  0  0  0  0  0  0  0  0  0
   -2.4699    0.9892    1.0923 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  1  0
  5  6  1  0
  6  7  2  0
  6  8  1  0
  3  9  1  0
  4 10  1  0
  4 11  1  0
  5 12  1  0
  5 13  1  0
  8 14  1  0
M  END
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PDB for #<Metabolite:0x00007f5a9c47ddc8>

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  O   UNK     0       3.907   0.385   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0      10.575  -0.385   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       5.240  -1.925   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0       9.241   1.925   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       6.574   0.385   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       7.907  -0.385   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       5.240  -0.385   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       9.241   0.385   0.000  0.00  0.00           C+0
CONECT    1    7                                                            
CONECT    2    8                                                            
CONECT    3    7                                                            
CONECT    4    8                                                            
CONECT    5    6    7                                                       
CONECT    6    5    8                                                       
CONECT    7    1    3    5                                                  
CONECT    8    2    4    6                                                  
MASTER        0    0    0    0    0    0    0    0    8    0   14    0
END
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3D PDB for #<Metabolite:0x00007f5a9c47ddc8>

COMPND    HMDB0000254
HETATM    1  O1  UNL     1       2.869   0.789  -0.736  1.00  0.00           O  
HETATM    2  C1  UNL     1       1.903   0.227  -0.164  1.00  0.00           C  
HETATM    3  O2  UNL     1       2.175  -0.496   0.988  1.00  0.00           O  
HETATM    4  C2  UNL     1       0.543   0.360  -0.738  1.00  0.00           C  
HETATM    5  C3  UNL     1      -0.398  -0.419   0.163  1.00  0.00           C  
HETATM    6  C4  UNL     1      -1.789  -0.381  -0.277  1.00  0.00           C  
HETATM    7  O3  UNL     1      -2.159  -1.095  -1.246  1.00  0.00           O  
HETATM    8  O4  UNL     1      -2.754   0.413   0.319  1.00  0.00           O  
HETATM    9  H1  UNL     1       1.665  -0.207   1.824  1.00  0.00           H  
HETATM   10  H2  UNL     1       0.459  -0.094  -1.751  1.00  0.00           H  
HETATM   11  H3  UNL     1       0.238   1.420  -0.846  1.00  0.00           H  
HETATM   12  H4  UNL     1      -0.012  -1.467   0.173  1.00  0.00           H  
HETATM   13  H5  UNL     1      -0.270  -0.040   1.199  1.00  0.00           H  
HETATM   14  H6  UNL     1      -2.470   0.989   1.092  1.00  0.00           H  
CONECT    1    2    2
CONECT    2    3    4
CONECT    3    9
CONECT    4    5   10   11
CONECT    5    6   12   13
CONECT    6    7    7    8
CONECT    8   14
END
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SMILES for #<Metabolite:0x00007f5a9c47ddc8>

OC(=O)CCC(O)=O
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INCHI for #<Metabolite:0x00007f5a9c47ddc8>

InChI=1S/C4H6O4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)(H,7,8)
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Synonyms
ValueSource
1,2-Ethanedicarboxylic acidChEBI
Acide butanedioiqueChEBI
Acide succiniqueChEBI
Acidum succinicumChEBI
Amber acidChEBI
AsuccinChEBI
BernsteinsaeureChEBI
ButandisaeureChEBI
Butanedionic acidChEBI
Dihydrofumaric acidChEBI
e363ChEBI
Ethylenesuccinic acidChEBI
HOOC-CH2-CH2-COOHChEBI
Spirit OF amberChEBI
1,2-EthanedicarboxylateGenerator
ButanedionateGenerator
DihydrofumarateGenerator
EthylenesuccinateGenerator
SuccinateGenerator
1,2 Ethanedicarboxylic acidMeSH
1,4 Butanedioic acidMeSH
1,4-Butanedioic acidMeSH
Ammonium succinateMeSH
Butanedioic acidMeSH
Potassium succinateMeSH
Succinate, ammoniumMeSH
Succinate, potassiumMeSH
1,4-ButanedioateHMDB
KatasuccinHMDB
Wormwood acidHMDB
2-Acetamido-2-deoxy-D-glucoseChEBI, HMDB
D-GlcNAcChEBI, HMDB
N-Acetyl-D-glucosamineChEBI, HMDB
N-AcetylchitosamineChEBI, HMDB
N Acetyl D glucosamineHMDB
2 Acetamido 2 deoxy D glucoseHMDB
2 Acetamido 2 deoxyglucoseHMDB
2-Acetamido-2-deoxyglucoseHMDB
AcetylglucosamineHMDB
Molecular FormulaC4H6O4
Average Mass118.088
Monoisotopic Mass118.02660868
IUPAC Namebutanedioic acid
Traditional Namesuccinic acid
CAS Registry Number110-15-6
SMILES
OC(=O)CCC(O)=O
InChI Identifier
InChI=1S/C4H6O4/c5-3(6)1-2-4(7)8/h1-2H2,(H,5,6)(H,7,8)
InChI KeyKDYFGRWQOYBRFD-UHFFFAOYSA-N