MiMeDB: Showing metabocard for (1R,6R)-6-Hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate (MMDBc0029943)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:47:46 UTC

Update Date

2022-08-31 17:37:50 UTC

Metabolite ID

MMDBc0029943

Metabolite Identification

Common Name

(1R,6R)-6-Hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate

Description

2-succinyl-6-hydroxy-2,4-cyclohexadiene-1-carboxylic acid (SHCHC) is the first identified intermediate in the menaquinone biosynthetic pathway. This pathway requires two reactions. They are the decarboxylation of alpha-ketoglutarate by an alpha-ketoglutarate decarboxylase, which results in the formation of succinic semialdehyde-thiamine PPi (TPP) anion, and the addition of the succinic semialdehyde-TPP anion to isochorismate carried out by the enzyme SHCHC synthase. In E. coli, addition of succinic semialdehyde-TPP anion (from 2-oxoglutarate) to isochorismate results in the formation of 2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate (SEPHCHC). In the subsequent reaction, the pyruvoyl group is eliminated, resulting in the prearomatic compound (1R,6R)-6-hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate (SHCHC). This is then aromatized to the benzenoid aromatic compound o-succinylbenzoate (OSB) and used as the framework for the construction of the rest of the menaquinone molecule. In this pathway, prenylation in the last step leads to the formation of 1,4-dihydroxy-2-naphtoic acid (DHNA). Subsequently OSB and DHNA formed in this pathway are incorporated into the naphthoquinone ring of menaquinone. SEPHCHC is an unstable compound and in mildly basic solutions, spontaneously undergoes a 2,5-elimination reaction resulting in the formation SHCHC and pyruvate. But the in vivo conversion of SEPHCHC to SHCHC is carried out by SHCHC synthase MenH. Dehydration from SHCHC by the enzyme OSB synthase (MenC) leads to the formation of the benzenoid aromatic compound OSB. The conversion of the benzenoid aromatic compound OSB to the naphthalenoid aromatic compound DHNA is catalyzed by the enzyme OSB-CoA synthetase (MenE). The process has been shown to have an absolute requirement for ATP and CoA. OSB-CoA is suggested as an intermediate. During the formation of OSB-CoA, ATP is hydrolyzed to AMP and PPi.

Structure

MOL SDF PDB SMILES InChI

      
  Mrv1533005211517342D          

 19 19  0  0  0  0            999 V2000
    1.4289    1.4437    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    1.0312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    1.0312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.2062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -2.1434    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.2062    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.4289   -1.0312    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.8578   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8578   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.0312    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.1434   -1.4437    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144   -1.4437    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.1434   -0.6187    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144   -0.6187    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  1  2  0  0  0  0
  5  4  1  0  0  0  0
  6  2  2  0  0  0  0
  7  4  1  0  0  0  0
  7  6  1  0  0  0  0
  8  3  1  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
 10  8  1  0  0  0  0
 10 11  1  6  0  0  0
 12  7  2  0  0  0  0
  8 13  1  1  0  0  0
 14  9  2  0  0  0  0
 15  9  1  0  0  0  0
 16 11  2  0  0  0  0
 17 11  1  0  0  0  0
  8 18  1  6  0  0  0
 10 19  1  1  0  0  0
M  CHG  2  15  -1  17  -1
M  END
> <DATABASE_ID>
MMDBc0029943

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@]1(O)C=CC=C(C(=O)CCC([O-])=O)[C@@]1([H])C([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C11H12O6/c12-7(4-5-9(14)15)6-2-1-3-8(13)10(6)11(16)17/h1-3,8,10,13H,4-5H2,(H,14,15)(H,16,17)/p-2/t8-,10-/m1/s1

> <INCHI_KEY>
QJYRAJSESKVEAE-PSASIEDQSA-L

> <FORMULA>
C11H10O6

> <MOLECULAR_WEIGHT>
238.196

> <EXACT_MASS>
238.048835202

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
21.524005021189826

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(1R,6R)-2-(3-carboxylatopropanoyl)-6-hydroxycyclohexa-2,4-diene-1-carboxylate

> <ALOGPS_LOGP>
0.24

> <JCHEM_LOGP>
-0.3190482766666666

> <ALOGPS_LOGS>
-1.26

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.340411281613099

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.6252125068265872

> <JCHEM_PKA_STRONGEST_BASIC>
-3.1354871525896746

> <JCHEM_POLAR_SURFACE_AREA>
117.56

> <JCHEM_REFRACTIVITY>
79.5584

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.50e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(1R,6R)-2-(3-carboxylatopropanoyl)-6-hydroxycyclohexa-2,4-diene-1-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 21-MAY-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   21-MAY-15         0                                  
HETATM    1  C   UNK     0       2.667   2.695   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334   1.925   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       4.001   1.925   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -1.334   0.385   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667  -0.385   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       1.334   0.385   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000  -0.385   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       4.001   0.385   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.001   0.385   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       2.667  -0.385   0.000  0.00  0.00           C+0
HETATM   11  C   UNK     0       2.667  -1.925   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0       0.000  -1.925   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       5.335  -0.385   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0      -5.335  -0.385   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -4.001   1.925   0.000  0.00  0.00           O-1
HETATM   16  O   UNK     0       4.001  -2.695   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.334  -2.695   0.000  0.00  0.00           O-1
HETATM   18  H   UNK     0       4.001  -1.155   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       1.334  -1.155   0.000  0.00  0.00           H+0
CONECT    1    2    3                                                       
CONECT    2    1    6                                                       
CONECT    3    1    8                                                       
CONECT    4    5    7                                                       
CONECT    5    4    9                                                       
CONECT    6    2    7   10                                                  
CONECT    7    4    6   12                                                  
CONECT    8    3   10   13   18                                             
CONECT    9    5   14   15                                                  
CONECT   10    6    8   11   19                                             
CONECT   11   10   16   17                                                  
CONECT   12    7                                                            
CONECT   13    8                                                            
CONECT   14    9                                                            
CONECT   15    9                                                            
CONECT   16   11                                                            
CONECT   17   11                                                            
CONECT   18    8                                                            
CONECT   19   10                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

Synonyms

Value	Source
(1R,6R)-6-Hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylate	ChEBI
(1R,6R)-6-Hydroxy-2-succinyl-cyclohexa-2,4-diene-1-carboxylic acid	Generator
(1R,6R)-6-Hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylic acid	Generator

Molecular Formula

C₁₁H₁₀O₆

Average Mass

238.196

Monoisotopic Mass

238.048835202

IUPAC Name

(1R,6R)-2-(3-carboxylatopropanoyl)-6-hydroxycyclohexa-2,4-diene-1-carboxylate

Traditional Name

(1R,6R)-2-(3-carboxylatopropanoyl)-6-hydroxycyclohexa-2,4-diene-1-carboxylate

CAS Registry Number

Not Available

SMILES

[H][C@@]1(O)C=CC=C(C(=O)CCC([O-])=O)[C@@]1([H])C([O-])=O

InChI Identifier

InChI=1S/C11H12O6/c12-7(4-5-9(14)15)6-2-1-3-8(13)10(6)11(16)17/h1-3,8,10,13H,4-5H2,(H,14,15)(H,16,17)/p-2/t8-,10-/m1/s1

InChI Key

QJYRAJSESKVEAE-PSASIEDQSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as gamma-keto acids and derivatives. These are organic compounds containing an aldehyde substituted with a keto group on the C4 carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Keto acids and derivatives

Sub Class

Gamma-keto acids and derivatives

Direct Parent

Gamma-keto acids and derivatives

Alternative Parents

Substituents

Gamma-keto acid
Beta-hydroxy acid
Short-chain keto acid
Dicarboxylic acid or derivatives
Hydroxy acid
Secondary alcohol
Ketone
Carboxylic acid
Carboxylic acid derivative
Organooxygen compound
Organic oxide
Alcohol
Carbonyl group
Organic oxygen compound
Hydrocarbon derivative
Organic anion
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

dicarboxylic acid dianion (CHEBI:58689 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	15 g/L	ALOGPS
logP	0.24	ALOGPS
logP	-0.32	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	3.63	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	117.56 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	79.56 m³·mol⁻¹	ChemAxon
Polarizability	21.52 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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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	73	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Chicken	Unknown
Bacteria	Firmicutes	7	Human feces; Human
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

Not Available

PDB ID

Not Available

ChEBI ID

58689

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 (1R,6R)-6-Hydroxy-2-succinylcyclohexa-2,4-diene-1-carboxylate (MMDBc0029943)

MOL for #<Metabolite:0x00007fed141ed490>

3D MOL for #<Metabolite:0x00007fed141ed490>

3D SDF for #<Metabolite:0x00007fed141ed490>

3D-SDF for #<Metabolite:0x00007fed141ed490>

PDB for #<Metabolite:0x00007fed141ed490>

3D PDB for #<Metabolite:0x00007fed141ed490>

SMILES for #<Metabolite:0x00007fed141ed490>

INCHI for #<Metabolite:0x00007fed141ed490>

Structure for #<Metabolite:0x00007fed141ed490>

3D Structure for #<Metabolite:0x00007fed141ed490>