MiMeDB: Showing metabocard for Isochorismate (MMDBc0030071)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:52:49 UTC

Update Date

2022-08-31 17:39:29 UTC

Metabolite ID

MMDBc0030071

Metabolite Identification

Common Name

Isochorismate

Description

Isochorismate is a member of the chemical class known as Beta Hydroxy Acids and Derivatives. These are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom. In Escherichia coli, isochorismate is a common precursor for the biosynthesis of the siderophore enterobactin and menaquinone (vitamin K2). Isochorismate is formed by the shikimate pathway from chorismate by the enzyme isochorismate synthase encoded by the entC gene. (PMID 8655506 )

Structure

MOL SDF PDB SMILES InChI

      
  Mrv1533005211517292D          

 18 18  0  0  0  0            999 V2000
   -1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.0000    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.7144    0.4125    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.4125    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    1.2375    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.8578    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.1434    1.2375    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.8578    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289    0.8250    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  2  1  0  0  0  0
  4  2  2  0  0  0  0
  5  1  2  0  0  0  0
  6  3  2  0  0  0  0
  7  4  1  0  0  0  0
  8  6  1  0  0  0  0
  8  7  1  0  0  0  0
  9  5  1  0  0  0  0
 10  6  1  0  0  0  0
  8 11  1  1  0  0  0
 12  9  2  0  0  0  0
 13  9  1  0  0  0  0
 14 10  1  0  0  0  0
 15 10  2  0  0  0  0
 16  5  1  0  0  0  0
  7 16  1  6  0  0  0
  7 17  1  1  0  0  0
  8 18  1  6  0  0  0
M  CHG  2  13  -1  14  -1
M  END
> <DATABASE_ID>
MMDBc0030071

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H10O6/c1-5(9(12)13)16-7-4-2-3-6(8(7)11)10(14)15/h2-4,7-8,11H,1H2,(H,12,13)(H,14,15)/p-2/t7-,8-/m0/s1

> <INCHI_KEY>
NTGWPRCCOQCMGE-YUMQZZPRSA-L

> <FORMULA>
C10H8O6

> <MOLECULAR_WEIGHT>
224.169

> <EXACT_MASS>
224.033185137

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
19.45753326302887

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
1

> <JCHEM_IUPAC>
(5S,6S)-5-[(1-carboxylatoeth-1-en-1-yl)oxy]-6-hydroxycyclohexa-1,3-diene-1-carboxylate

> <ALOGPS_LOGP>
0.64

> <JCHEM_LOGP>
-0.12549059733333331

> <ALOGPS_LOGS>
-1.27

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
4.193366544817536

> <JCHEM_PKA_STRONGEST_ACIDIC>
3.389432923694941

> <JCHEM_PKA_STRONGEST_BASIC>
-3.571763680746476

> <JCHEM_POLAR_SURFACE_AREA>
109.72000000000001

> <JCHEM_REFRACTIVITY>
75.9843

> <JCHEM_ROTATABLE_BOND_COUNT>
4

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.39e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
isochorismate

> <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  -1.540   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       1.334  -2.310   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.667  -1.540   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000  -1.540   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -2.667   0.000   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       2.667   0.000   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       1.334   0.770   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      -4.001   0.770   0.000  0.00  0.00           C+0
HETATM   10  C   UNK     0       4.001   0.770   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0       1.334   2.310   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -5.335   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -4.001   2.310   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       4.001   2.310   0.000  0.00  0.00           O-1
HETATM   15  O   UNK     0       5.335   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -1.334   0.770   0.000  0.00  0.00           O+0
HETATM   17  H   UNK     0       0.000   1.540   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       2.667   1.540   0.000  0.00  0.00           H+0
CONECT    1    5                                                            
CONECT    2    3    4                                                       
CONECT    3    2    6                                                       
CONECT    4    2    7                                                       
CONECT    5    1    9   16                                                  
CONECT    6    3    8   10                                                  
CONECT    7    4    8   16   17                                             
CONECT    8    6    7   11   18                                             
CONECT    9    5   12   13                                                  
CONECT   10    6   14   15                                                  
CONECT   11    8                                                            
CONECT   12    9                                                            
CONECT   13    9                                                            
CONECT   14   10                                                            
CONECT   15   10                                                            
CONECT   16    5    7                                                       
CONECT   17    7                                                            
CONECT   18    8                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

Synonyms

Value	Source
Isochorismic acid	Generator
5-((1-Carboxyethenyl)oxy)-6-hydroxy-1,3-cyclohexadiene-1-carboxylic acid	MeSH
Iso-chorismic acid	MeSH

Molecular Formula

C₁₀H₈O₆

Average Mass

224.169

Monoisotopic Mass

224.033185137

IUPAC Name

(5S,6S)-5-[(1-carboxylatoeth-1-en-1-yl)oxy]-6-hydroxycyclohexa-1,3-diene-1-carboxylate

Traditional Name

isochorismate

CAS Registry Number

22642-82-6

SMILES

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

InChI Identifier

InChI=1S/C10H10O6/c1-5(9(12)13)16-7-4-2-3-6(8(7)11)10(14)15/h2-4,7-8,11H,1H2,(H,12,13)(H,14,15)/p-2/t7-,8-/m0/s1

InChI Key

NTGWPRCCOQCMGE-YUMQZZPRSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Beta hydroxy acids and derivatives

Direct Parent

Beta hydroxy acids and derivatives

Alternative Parents

Substituents

Beta-hydroxy acid
Dicarboxylic acid or derivatives
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Organic anion
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

dicarboxylic acid dianion (CHEBI:29780 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	13.9 g/L	ALOGPS
logP	0.64	ALOGPS
logP	-0.13	ChemAxon
logS	-1.3	ALOGPS
pKa (Strongest Acidic)	3.39	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	1	ChemAxon
Polar Surface Area	109.72 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	75.98 m³·mol⁻¹	ChemAxon
Polarizability	19.46 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	Splash Key	Deposition Date	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-004i-0090000000-d0e1b69e1037e00ab29d	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-016r-0390000000-0a87369042d47ddfe4a9	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-02bf-9510000000-4ea64c0fdf3611dbb8b6	2017-07-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00di-0090000000-4aeb7c2964ad49690938	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-00di-0290000000-36edda281e55b184cbbf	2017-07-26	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-03dr-9800000000-d3d8134172375fd21a93	2017-07-26	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-20	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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
MMDBr0007142	Oxoglutaric acid	2-Succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate	Not Available	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylic-acid synthase	VMH	30371894
MMDBr0007875	Chorismate	Isochorismate	Not Available	Isochorismate synthase	VMH	30371894
MMDBr0012977	Water	(2S,3S)-2,3-dihydroxy-2,3-dihydrobenzoic acid	Isochorismatase	Synthesis	RHEA	34755880
MMDBr0013825	Chorismate	Isochorismate	Isochorismate synthase DhbC	Synthesis	RHEA	34755880
MMDBr0014566	alpha-Ketoglutarate	5-enolpyruvoyl-6-hydroxy-2-succinyl-cyclohex-3-ene-1-carboxylic acid	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase	Synthesis	RHEA	34755880
MMDBr0014746	Isochorismate	Pyruvic acid	Salicylate synthase	Non-hydrolytic bond cleavage (or its reversal); Synthesis	RHEA	34755880
MMDBr0018033	Water	Pyruvic acid	Enterobactin synthase component B	Synthesis	PathBank	31602464
MMDBr0018884	Oxoglutaric acid	Carbon dioxide	2-succinyl-5-enolpyruvyl-6-hydroxy-3-cyclohexene-1-carboxylate synthase	Synthesis	PathBank	31602464
MMDBr0019240	Water	Pyruvic acid	Enterobactin synthase component B	Synthesis	PathBank	31602464

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	204	Pig ; Human feces; Human ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Human stool; Human sputum; Chicken ; Cattle ; River trout	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	122	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human nasopharyngeal swab; Human mucosa; Human supragingival plaque; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Firmicutes	168	Human feces; Human ; Human subgingival plaque; Cattle	Metabolic reconstruction
Bacteria	Bacteroidetes	107	Human feces; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Archaea	Euryarchaeota	1		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1
Bacteria	Cyanobacteria	30	Human
Bacteria	Chloroflexi	3
Bacteria	Chlorobi	10
Archaea/Archaea	Euryarchaeota	6		Metabolic reconstruction
Bacteria	Chlamydiae	1	Human
Bacteria	nah	1
Bacteria/NULL	Proteobacteria	1	Pig ; Human feces; Human ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal; Human stool; Human sputum; Chicken ; Cattle ; River trout	Unknown; Metabolic reconstruction

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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

DB02793

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

29780

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
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 Isochorismate (MMDBc0030071)

MOL for #<Metabolite:0x00007f5abcb38e90>

3D MOL for #<Metabolite:0x00007f5abcb38e90>

3D SDF for #<Metabolite:0x00007f5abcb38e90>

3D-SDF for #<Metabolite:0x00007f5abcb38e90>

PDB for #<Metabolite:0x00007f5abcb38e90>

3D PDB for #<Metabolite:0x00007f5abcb38e90>

SMILES for #<Metabolite:0x00007f5abcb38e90>

INCHI for #<Metabolite:0x00007f5abcb38e90>

Structure for #<Metabolite:0x00007f5abcb38e90>

3D Structure for #<Metabolite:0x00007f5abcb38e90>