MiMeDB: Showing metabocard for 5-O-(1-Carboxyvinyl)-3-phosphoshikimate (MMDBc0030030)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:51:17 UTC

Update Date

2022-08-31 17:38:52 UTC

Metabolite ID

MMDBc0030030

Metabolite Identification

Common Name

5-O-(1-Carboxyvinyl)-3-phosphoshikimate

Description

5-o-(1-carboxyvinyl)-3-phosphoshikimate is a member of the chemical class known as Organophosphate Esters. These are organic compounds containing phosphoric acid ester functional group. The shikimate pathway enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is the target of the broad spectrum herbicide glyphosate. (PMID 19211556 ) 5-Enolpyruvylshikimate-3-phosphate (EPSP) synthase (AroA) is a key enzyme in the aromatic amino acid biosynthetic pathway in microorganisms and plants, and is the target of the herbicide glyphosate. (PMID 16469313 )

Structure

MOL SDF PDB SMILES InChI

 
  Mrv0541 02241222162D          
 
 21 21  0  0  1  0            999 V2000
   10.5979  -10.5386    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   11.4222  -10.5386    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.7810  -10.5425    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5979   -9.7180    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.5979  -11.3630    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0957  -10.1340    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.8104  -10.5538    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.0957   -9.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5328  -10.1340    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   12.8067  -11.3744    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.8104   -8.8899    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.2812  -10.5462    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.5328   -9.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   12.8067   -8.0692    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9959  -10.1340    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   13.5214   -7.6983    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0920   -7.7021    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.7068  -10.5462    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.9959   -9.4333    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.4216  -10.1340    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.7068  -11.3668    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  0  0  0  0
  1  5  2  0  0  0  0
  6  2  1  6  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  7  9  1  0  0  0  0
  7 10  1  6  0  0  0
  8 11  2  0  0  0  0
  9 12  1  1  0  0  0
  9 13  1  0  0  0  0
 11 14  1  0  0  0  0
 12 15  1  0  0  0  0
 14 16  1  0  0  0  0
 14 17  2  0  0  0  0
 15 18  1  0  0  0  0
 15 19  2  0  0  0  0
 18 20  1  0  0  0  0
 18 21  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030030

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C10H13O10P/c1-4(9(12)13)19-6-2-5(10(14)15)3-7(8(6)11)20-21(16,17)18/h3,6-8,11H,1-2H2,(H,12,13)(H,14,15)(H2,16,17,18)/t6-,7-,8+/m1/s1

> <INCHI_KEY>
QUTYKIXIUDQOLK-PRJMDXOYSA-N

> <FORMULA>
C10H13O10P

> <MOLECULAR_WEIGHT>
324.178

> <EXACT_MASS>
324.024633148

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
26.128505477215874

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5R)-5-[(1-carboxyeth-1-en-1-yl)oxy]-4-hydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylic acid

> <ALOGPS_LOGP>
-0.83

> <JCHEM_LOGP>
-1.117946039

> <ALOGPS_LOGS>
-1.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
3.3844668615812927

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3139497715846575

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6352106700092754

> <JCHEM_POLAR_SURFACE_AREA>
170.82

> <JCHEM_REFRACTIVITY>
65.5819

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.63e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4S,5R)-5-[(1-carboxyeth-1-en-1-yl)oxy]-4-hydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  P   UNK     0      19.783 -19.672   0.000  0.00  0.00           P+0
HETATM    2  O   UNK     0      21.321 -19.672   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0      18.258 -19.679   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      19.783 -18.140   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0      19.783 -21.211   0.000  0.00  0.00           O+0
HETATM    6  C   UNK     0      22.579 -18.917   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      23.913 -19.700   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0      22.579 -17.364   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0      25.261 -18.917   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0      23.906 -21.232   0.000  0.00  0.00           O+0
HETATM   11  C   UNK     0      23.913 -16.594   0.000  0.00  0.00           C+0
HETATM   12  O   UNK     0      26.658 -19.686   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      25.261 -17.364   0.000  0.00  0.00           C+0
HETATM   14  C   UNK     0      23.906 -15.063   0.000  0.00  0.00           C+0
HETATM   15  C   UNK     0      27.992 -18.917   0.000  0.00  0.00           C+0
HETATM   16  O   UNK     0      25.240 -14.370   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      22.572 -14.377   0.000  0.00  0.00           O+0
HETATM   18  C   UNK     0      29.319 -19.686   0.000  0.00  0.00           C+0
HETATM   19  C   UNK     0      27.992 -17.609   0.000  0.00  0.00           C+0
HETATM   20  O   UNK     0      30.654 -18.917   0.000  0.00  0.00           O+0
HETATM   21  O   UNK     0      29.319 -21.218   0.000  0.00  0.00           O+0
CONECT    1    2    3    4    5                                             
CONECT    2    1    6                                                       
CONECT    3    1                                                            
CONECT    4    1                                                            
CONECT    5    1                                                            
CONECT    6    2    7    8                                                  
CONECT    7    6    9   10                                                  
CONECT    8    6   11                                                       
CONECT    9    7   12   13                                                  
CONECT   10    7                                                            
CONECT   11    8   14   13                                                  
CONECT   12    9   15                                                       
CONECT   13    9   11                                                       
CONECT   14   11   16   17                                                  
CONECT   15   12   18   19                                                  
CONECT   16   14                                                            
CONECT   17   14                                                            
CONECT   18   15   20   21                                                  
CONECT   19   15                                                            
CONECT   20   18                                                            
CONECT   21   18                                                            
MASTER        0    0    0    0    0    0    0    0   21    0   42    0
END

Synonyms

Value	Source
O5-(1-Carboxyvinyl)-3-phosphoshikimate	ChEBI
O5-(1-Carboxyvinyl)-3-phosphoshikimic acid	Generator
5-O-(1-Carboxyvinyl)-3-phosphoshikimic acid	Generator
5-O-(1-Carboxyvinyl)-3-phosphoshikimate	ChEBI, Generator

Molecular Formula

C₁₀H₁₃O₁₀P

Average Mass

324.178

Monoisotopic Mass

324.024633148

IUPAC Name

(3R,4S,5R)-5-[(1-carboxyeth-1-en-1-yl)oxy]-4-hydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylic acid

Traditional Name

(3R,4S,5R)-5-[(1-carboxyeth-1-en-1-yl)oxy]-4-hydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylic acid

CAS Registry Number

89771-75-5

SMILES

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

InChI Identifier

InChI=1S/C10H13O10P/c1-4(9(12)13)19-6-2-5(10(14)15)3-7(8(6)11)20-21(16,17)18/h3,6-8,11H,1-2H2,(H,12,13)(H,14,15)(H2,16,17,18)/t6-,7-,8+/m1/s1

InChI Key

QUTYKIXIUDQOLK-PRJMDXOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Organic phosphoric acids and derivatives

Sub Class

Phosphate esters

Direct Parent

Monoalkyl phosphates

Alternative Parents

Substituents

Monoalkyl phosphate
Dicarboxylic acid or derivatives
Cyclitol or derivatives
Secondary alcohol
Carboxylic acid
Carboxylic acid derivative
Organic oxygen compound
Organic oxide
Hydrocarbon derivative
Organooxygen compound
Carbonyl group
Alcohol
Aliphatic homomonocyclic compound

Molecular Framework

Aliphatic homomonocyclic compounds

External Descriptors

dicarboxylic acid (CHEBI:16257 )
phosphoshikimic acid (CHEBI:16257 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	5.63 g/L	ALOGPS
logP	-0.83	ALOGPS
logP	-1.1	ChemAxon
logS	-1.8	ALOGPS
pKa (Strongest Acidic)	1.31	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	170.82 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	65.58 m³·mol⁻¹	ChemAxon
Polarizability	26.13 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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

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	21	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Rat ; Turkey ; Sheep ; Lion ; Chicken ; Human subgingival plaque	Unknown; Metabolic reconstruction
Bacteria/Eubacteria	Firmicutes	409	Human feces; Human pleural fluid plaque; Pig ; Human ; Human stool; Human subgingival plaque; Cattle ; Catfish ; Human saliva	Metabolic reconstruction
Bacteria/Eubacteria	Proteobacteria	533	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal; Cattle ; River trout ; Rat ; Turkey ; Sheep ; Lion ; Chicken ; Human subgingival plaque	Unknown; Metabolic reconstruction
Bacteria	Actinobacteria	12	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Actinobacteria	152	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva; Cattle	Metabolic reconstruction
Bacteria/Eubacteria	Verrucomicrobia	3	Human ; Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Bacteroidetes	124	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	1	Human feces	Metabolic reconstruction
Bacteria/Eubacteria	Spirochaetes	9	Human feces; Human ; Pig	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction
Bacteria/Eubacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Bacteria	Firmicutes	23	Human feces; Human pleural fluid plaque; Pig ; Human ; Human stool; Human subgingival plaque; Cattle ; Catfish ; Human saliva	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria/Eubacteria	Planctomycetes	2	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Cyanobacteria	35	Human
Bacteria/Eubacteria	Acidobacteria	3
Archaea/Archaea	Crenarchaeota	17		Metabolic reconstruction
Bacteria/Eubacteria	Aquificae	3
Archaea/Archaea	Euryarchaeota	35		Metabolic reconstruction
Bacteria/Eubacteria	Chloroflexi	9
Bacteria/Eubacteria	Chlamydiae	10	Human ; Sheep ; Cat
Bacteria/Eubacteria	Chlorobi	11
Bacteria/Eubacteria	Deinococcus-thermus	4
Bacteria/Eubacteria	Elusimicrobia	1
Archaea/Archaea	Korarchaeota	1
Eukaryota/Fungi	Ascomycota	53	Human feces; Human saliva	Unknown
Bacteria	nah	1
Bacteria/Eubacteria	Thermotogae	5
Eukaryota/Fungi	Basidiomycota	7
Archaea/Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria/Eubacteria	Nitrospirae	1

Exposure Sources

Other Exposures

Source Type	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

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00007627

Chemspider ID

Not Available

KEGG Compound ID

C01269

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439463

PDB ID

Not Available

ChEBI ID

16257

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 ]
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 5-O-(1-Carboxyvinyl)-3-phosphoshikimate (MMDBc0030030)

MOL for #<Metabolite:0x00005645ca232b78>

3D MOL for #<Metabolite:0x00005645ca232b78>

3D SDF for #<Metabolite:0x00005645ca232b78>

3D-SDF for #<Metabolite:0x00005645ca232b78>

PDB for #<Metabolite:0x00005645ca232b78>

3D PDB for #<Metabolite:0x00005645ca232b78>

SMILES for #<Metabolite:0x00005645ca232b78>

INCHI for #<Metabolite:0x00005645ca232b78>

Structure for #<Metabolite:0x00005645ca232b78>

3D Structure for #<Metabolite:0x00005645ca232b78>