MiMeDB: Showing metabocard for 2-Succinylbenzoate (MMDBc0029982)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:49:20 UTC

Update Date

2022-08-31 17:38:19 UTC

Metabolite ID

MMDBc0029982

Metabolite Identification

Common Name

2-Succinylbenzoate

Description

2-succinylbenzoate is a member of the chemical class known as Benzoic Acid and Derivatives. These are organic compounds containing a carboxylic acid substituent attached to a benzene ring. 2-Succinylbenzoate is invovled in the biosynthesis of menaquinone. o-Succinylbenzoate synthase (OSBS) from Escherichia coli, a member of the enolase superfamily, catalyzes an exergonic dehydration reaction in the menaquinone biosynthetic pathway in which 2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylate (SHCHC) is converted to 4-(2'-carboxyphenyl)-4-oxobutyrate (o-succinylbenzoate or OSB). The first aromatic intermediate in the menaquinone biosynthetic pathway is o-succinylbenzoate (OSB); it is formed from chorismate/isochorismate and 2-ketoglutarate. (PMID 3902015 ) The first aromatic intermediate in the menaquinone biosynthetic pathway is o-succinylbenzoate (OSB); it is formed from chorismate/isochorismate and 2-ketoglutarate. The first aromatic intermediate in the menaquinone biosynthetic pathway is o-succinylbenzoate (OSB); it is formed from chorismate/isochorismate and 2-ketoglutarate. The first aromatic intermediate in the menaquinone biosynthetic pathway is o-succinylbenzoate (OSB); it is formed from chorismate/isochorismate and 2-ketoglutarate. coli strains synthesize an intermediate, "X", which is converted to OSB by extracts of menC+ cells. It was demonstrated that chorismate is the branch point compound leading to menaquinone, and that 2-succinylbenzoic acid and 1,4-dihydroxy-2-naphthoic acid can serve as menaquinoone precursors in E. coli. (PMID 1091286 ) The committed step in menaquinone biosynthesis is the formation of o-succinylbenzoate (OSB). (PMID 3516220 ) The suggestion is made that the spirodilactone is the product of an aberrant reaction involving a compound that is normally an intermediate in the conversion of 2-succinylbenzoate to 1,4-dihydroxy-2-naphthoate. (PMID 99177 ) The presence of shikimic acid in the growth medium restores the ability of an aroD mutant to synthesize cmo5U, while O-succinylbenzoate, which is an early intermediate in the synthesis of menaquinone, does not. (PMID 2104604 )

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 01211515262D          

 16 16  0  0  0  0            999 V2000
    5.0013    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    5.0013    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.2868    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724    4.5375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    3.3000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    3.7125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    4.9500    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7145    4.5375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.1434    4.5375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8579    5.7750    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
  2  1  2  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  2  0  0  0  0
  8  4  2  0  0  0  0
  8  7  1  0  0  0  0
  9  5  1  0  0  0  0
  9  7  1  0  0  0  0
 10  6  1  0  0  0  0
 11  8  1  0  0  0  0
 12  9  2  0  0  0  0
 13 10  2  0  0  0  0
 14 10  1  0  0  0  0
 15 11  2  0  0  0  0
 16 11  1  0  0  0  0
M  CHG  2  14  -1  16  -1
M  END
> <DATABASE_ID>
MMDBc0029982

> <DATABASE_NAME>
MIME

> <SMILES>
[O-]C(=O)CCC(=O)C1=CC=CC=C1C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H10O5/c12-9(5-6-10(13)14)7-3-1-2-4-8(7)11(15)16/h1-4H,5-6H2,(H,13,14)(H,15,16)/p-2

> <INCHI_KEY>
YIVWQNVQRXFZJB-UHFFFAOYSA-L

> <FORMULA>
C11H8O5

> <MOLECULAR_WEIGHT>
220.181

> <EXACT_MASS>
220.038270517

> <JCHEM_ACCEPTOR_COUNT>
5

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
20.064720897416933

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
2-(3-carboxylatopropanoyl)benzoate

> <ALOGPS_LOGP>
0.84

> <JCHEM_LOGP>
1.0133389896666665

> <ALOGPS_LOGS>
-2.02

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.595760241001752

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.4184310583310977

> <JCHEM_PKA_STRONGEST_BASIC>
-7.57018002288234

> <JCHEM_POLAR_SURFACE_AREA>
97.33000000000001

> <JCHEM_REFRACTIVITY>
76.28450000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.47e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-succinylbenzoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 21-JAN-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-JAN-15         0                                  
HETATM    1  C   UNK     0       9.336   6.930   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       9.336   8.470   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       8.002   6.160   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       8.002   9.240   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.001   6.930   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   6.160   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       6.668   6.930   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       6.668   8.470   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       5.335   6.160   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       1.334   6.930   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       5.335   9.240   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       5.335   4.620   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   6.160   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       1.334   8.470   0.000  0.00  0.00           O-1
HETATM   15  O   UNK     0       4.001   8.470   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       5.335  10.780   0.000  0.00  0.00           O-1
CONECT    1    2    3                                                       
CONECT    2    1    4                                                       
CONECT    3    1    7                                                       
CONECT    4    2    8                                                       
CONECT    5    6    9                                                       
CONECT    6    5   10                                                       
CONECT    7    3    8    9                                                  
CONECT    8    4    7   11                                                  
CONECT    9    5    7   12                                                  
CONECT   10    6   13   14                                                  
CONECT   11    8   15   16                                                  
CONECT   12    9                                                            
CONECT   13   10                                                            
CONECT   14   10                                                            
CONECT   15   11                                                            
CONECT   16   11                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   32    0
END

Synonyms

Value	Source
O-Succinatobenzoate	ChEBI
O-Succinylbenzoate	ChEBI
Succinylbenzoate	ChEBI
O-Succinatobenzoic acid	Generator
O-Succinylbenzoic acid	Generator
Succinylbenzoic acid	Generator
2-Succinylbenzoic acid	Generator
2-Succinylbenzoate	ChEBI
2-Succinatobenzoic acid	Generator

Molecular Formula

C₁₁H₈O₅

Average Mass

220.181

Monoisotopic Mass

220.038270517

IUPAC Name

2-(3-carboxylatopropanoyl)benzoate

Traditional Name

2-succinylbenzoate

CAS Registry Number

27415-09-4

SMILES

[O-]C(=O)CCC(=O)C1=CC=CC=C1C([O-])=O

InChI Identifier

InChI=1S/C11H10O5/c12-9(5-6-10(13)14)7-3-1-2-4-8(7)11(15)16/h1-4H,5-6H2,(H,13,14)(H,15,16)/p-2

InChI Key

YIVWQNVQRXFZJB-UHFFFAOYSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alkyl-phenylketones. These are aromatic compounds containing a ketone substituted by one alkyl group, and a phenyl group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Alkyl-phenylketones

Alternative Parents

Substituents

Alkyl-phenylketone
Butyrophenone
Benzoic acid or derivatives
Benzoic acid
Aryl alkyl ketone
Benzoyl
Gamma-keto acid
Monocyclic benzene moiety
Benzenoid
Dicarboxylic acid or derivatives
Keto acid
Carboxylic acid derivative
Carboxylic acid
Organic oxide
Hydrocarbon derivative
Organic anion
Aromatic homomonocyclic compound

Molecular Framework

Aromatic homomonocyclic compounds

External Descriptors

dicarboxylic acid dianion (CHEBI:18325 )
a small molecule (O-SUCCINYLBENZOATE )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	2.47 g/L	ALOGPS
logP	0.84	ALOGPS
logP	1.01	ChemAxon
logS	-2	ALOGPS
pKa (Strongest Acidic)	3.42	ChemAxon
pKa (Strongest Basic)	-7.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	97.33 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	76.28 m³·mol⁻¹	ChemAxon
Polarizability	20.06 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	Yes	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum

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

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0012867	(1R,6R)-6-Hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate	2-Succinylbenzoate	o-succinylbenzoate synthase	Racemization; Synthesis	RHEA	34755880
MMDBr0013602	2-Succinylbenzoate	2-Succinylbenzoyl-CoA	2-succinylbenzoate--CoA ligase	Ligation	RHEA	34755880
MMDBr0018887	(1R,6R)-6-Hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate	Water	o-succinylbenzoate synthase	Synthesis	PathBank	31602464
MMDBr0018888	Adenosine triphosphate	Adenosine monophosphate	2-succinylbenzoate--CoA ligase	Ligation	PathBank	31602464
MMDBr0038757	2-Succinylbenzoyl-CoA	2-Succinylbenzoate	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	Proteobacteria	70	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Chicken	Unknown
Bacteria	Firmicutes	44	Human feces; Human ; Cattle ; Human subgingival plaque; Human saliva
Bacteria	Actinobacteria	12	Cattle ; Human
Bacteria	nah	1
Bacteria	Cyanobacteria	1
Bacteria	Deinococcus-thermus	2

Exposure Sources

Source Type	Source Sub-type	Species	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

Not Available

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5459922

PDB ID

Not Available

ChEBI ID

18325

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Wishart DS, Li C, Marcu A, Badran H, Pon A, Budinski Z, Patron J, Lipton D, Cao X, Oler E, Li K, Paccoud M, Hong C, Guo AC, Chan C, Wei W, Ramirez-Gaona M: PathBank: a comprehensive pathway database for model organisms. Nucleic Acids Res. 2020 Jan 8;48(D1):D470-D478. doi: 10.1093/nar/gkz861. [PubMed:31602464 ]
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 2-Succinylbenzoate (MMDBc0029982)

MOL for #<Metabolite:0x00007f5a51ea2100>

3D MOL for #<Metabolite:0x00007f5a51ea2100>

3D SDF for #<Metabolite:0x00007f5a51ea2100>

3D-SDF for #<Metabolite:0x00007f5a51ea2100>

PDB for #<Metabolite:0x00007f5a51ea2100>

3D PDB for #<Metabolite:0x00007f5a51ea2100>

SMILES for #<Metabolite:0x00007f5a51ea2100>

INCHI for #<Metabolite:0x00007f5a51ea2100>

Structure for #<Metabolite:0x00007f5a51ea2100>

3D Structure for #<Metabolite:0x00007f5a51ea2100>