MiMeDB: Showing metabocard for Shikimate 3-phosphate (MMDBc0030096)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:53:45 UTC

Update Date

2022-08-31 17:39:41 UTC

MiMeDB ID

MMDBc0030096

Metabolite Identification

Common Name

Shikimate 3-phosphate

Description

Shikimate 3-phosphate is a member of the chemical class known as Organophosphate Esters. These are organic compounds containing phosphoric acid ester functional group. Shikimate 3-phosphate is involved in the shikimate pathway. The shikimate pathway enzyme 5-enolpyruvyl shikimate-3-phosphate synthase (EPSP synthase) has received attention in the past because it is the target of the broad-spectrum herbicide glyphosate. (PMID 16225867 ) The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) catalyzes the penultimate step of the shikimate pathway and is the target of the broad-spectrum herbicide glyphosate. (PMID 15736934 )

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303082008462D          

 19 19  0  0  0  0            999 V2000
   -0.3572   -1.3884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.1509    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572   -0.9759    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717   -0.9759    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.3572    0.2615    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.0717   -0.1509    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.0717   -1.3884    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7861   -1.3884    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7861    0.2615    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0717   -2.2134    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.7861   -0.9759    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.7861    1.9115    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.6592    2.2134    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -1.4842    0.7845    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3572    1.0865    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    1.4990    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7861   -0.5634    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3572    0.6740    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -1.0717    0.6740    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  3  2  2  0  0  0  0
  4  1  1  0  0  0  0
  5  2  1  0  0  0  0
  6  4  1  0  0  0  0
  6  5  1  0  0  0  0
  7  3  1  0  0  0  0
  4  8  1  1  0  0  0
  6  9  1  6  0  0  0
 10  7  2  0  0  0  0
 11  7  1  0  0  0  0
  5 15  1  6  0  0  0
 16 12  1  0  0  0  0
 16 13  1  0  0  0  0
 16 14  2  0  0  0  0
 16 15  1  0  0  0  0
  4 17  1  6  0  0  0
  5 18  1  1  0  0  0
  6 19  1  1  0  0  0
M  CHG  3  11  -1  12  -1  13  -1
M  END
> <DATABASE_ID>
MMDBc0030096

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C7H11O8P/c8-4-1-3(7(10)11)2-5(6(4)9)15-16(12,13)14/h2,4-6,8-9H,1H2,(H,10,11)(H2,12,13,14)/p-3/t4-,5-,6+/m1/s1

> <INCHI_KEY>
QYOJSKGCWNAKGW-PBXRRBTRSA-K

> <FORMULA>
C7H8O8P

> <MOLECULAR_WEIGHT>
251.108

> <EXACT_MASS>
250.997324955

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
24

> <JCHEM_AVERAGE_POLARIZABILITY>
19.397534158462594

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-3

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4S,5R)-4,5-dihydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylate

> <ALOGPS_LOGP>
-1.54

> <JCHEM_LOGP>
-1.7636401083333335

> <ALOGPS_LOGS>
-0.73

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
4.1018283495734575

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3157644234401227

> <JCHEM_PKA_STRONGEST_BASIC>
-3.225778459939349

> <JCHEM_POLAR_SURFACE_AREA>
153.01

> <JCHEM_REFRACTIVITY>
58.4269

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.70e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4S,5R)-4,5-dihydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 08-MAR-20   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   08-MAR-20         0                                  
HETATM    1  C   UNK     0      -0.667  -2.592   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.667  -0.282   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.667  -1.822   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -2.001  -1.822   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      -0.667   0.488   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -2.001  -0.282   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       2.001  -2.592   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -3.334  -2.592   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -3.334   0.488   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       2.001  -4.132   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.334  -1.822   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0      -3.334   3.568   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0      -1.231   4.132   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0      -2.771   1.464   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0      -0.667   2.028   0.000  0.00  0.00           O+0
HETATM   16  P   UNK     0      -2.001   2.798   0.000  0.00  0.00           P+0
HETATM   17  H   UNK     0      -3.334  -1.052   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       0.667   1.258   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0      -2.001   1.258   0.000  0.00  0.00           H+0
CONECT    1    3    4                                                       
CONECT    2    3    5                                                       
CONECT    3    1    2    7                                                  
CONECT    4    1    6    8   17                                             
CONECT    5    2    6   15   18                                             
CONECT    6    4    5    9   19                                             
CONECT    7    3   10   11                                                  
CONECT    8    4                                                            
CONECT    9    6                                                            
CONECT   10    7                                                            
CONECT   11    7                                                            
CONECT   12   16                                                            
CONECT   13   16                                                            
CONECT   14   16                                                            
CONECT   15    5   16                                                       
CONECT   16   12   13   14   15                                             
CONECT   17    4                                                            
CONECT   18    5                                                            
CONECT   19    6                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   38    0
END

Synonyms

Value	Source
3-Phosphonatoshikimate trianion	ChEBI
3-Phosphoshikimate	ChEBI
3-Phosphonatoshikimic acid trianion	Generator
3-Phosphoshikimic acid	Generator
Shikimic acid 3-phosphoric acid	Generator
3-Phosphonatoshikimic acid(3-)	Generator

Chemical Formula

C₇H₈O₈P

Average Molecular Weight

251.108

Monoisotopic Molecular Weight

250.997324955

IUPAC Name

(3R,4S,5R)-4,5-dihydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylate

Traditional Name

(3R,4S,5R)-4,5-dihydroxy-3-(phosphonooxy)cyclohex-1-ene-1-carboxylate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C7H11O8P/c8-4-1-3(7(10)11)2-5(6(4)9)15-16(12,13)14/h2,4-6,8-9H,1H2,(H,10,11)(H2,12,13,14)/p-3/t4-,5-,6+/m1/s1

InChI Key

QYOJSKGCWNAKGW-PBXRRBTRSA-K

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as alkyl phosphates. These are organic compounds containing a phosphate group that is linked to one or more alkyl chains.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Organic phosphoric acids and derivatives

Sub Class

Phosphate esters

Direct Parent

Alkyl phosphates

Alternative Parents

Substituents

Alkyl phosphate
Cyclitol or derivatives
Secondary alcohol
1,2-diol
Monocarboxylic acid or derivatives
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

hydroxy monocarboxylic acid anion (CHEBI:145989 )
organophosphate oxoanion (CHEBI:145989 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	57 g/L	ALOGPS
logP	-1.5	ALOGPS
logP	-1.8	ChemAxon
logS	-0.73	ALOGPS
pKa (Strongest Acidic)	1.32	ChemAxon
pKa (Strongest Basic)	-3.2	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	153.01 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	58.43 m³·mol⁻¹	ChemAxon
Polarizability	19.4 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

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

Proteins

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Related Health Condition	Evidence Type	Measured in Matrix	Data Source	Reference

Microbial Sources

Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
	Proteobacteria	350	Human ; Pig ; Cattle ; Turkey ; Lion ; Chicken ; Human Feces; Rat	Unknown;
Fungi	Ascomycota	53	Human Feces	; Unknown
Fungi	Basidiomycota	7
	Actinobacteria	36	Human ; Cattle ; Human Feces
Archaea	Crenarchaeota	9
	Firmicutes	136	Human Feces; Human ; Catfish ; Cattle
	Aquificae	3
Archaea	Euryarchaeota	32
	Bacteroidetes	9	Human
	Chlorobi	11
	Chlamydiae	9	Human ; Cat
	Chloroflexi	9
	Deinococcus-Thermus	4
	Dictyoglomi	1
	Fusobacteria	1	Human
	Cyanobacteria	31	Human
	Spirochaetes	7	Human ; Pig
	Verrucomicrobia	3	Human
	Euryarchaeota	2	Human Feces; Human
	Planctomycetes	1
		1
	Nitrospirae	1
NULL	Proteobacteria	2
	Thermotogae	5
	Elusimicrobia	1
Archaea	Korarchaeota	1
	Acidobacteria	2
Archaea	Thaumarchaeota	1
	Crenarchaeota	1	Human Feces

Exposure Sources

Source Type	Source Sub-type	Species	Data Source	Reference	Details

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

23092113

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

14506806

PDB ID

Not Available

ChEBI ID

145989

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 Shikimate 3-phosphate (MMDBc0030096)

MOL for #<Metabolite:0x0000564abbfaed10>

3D MOL for #<Metabolite:0x0000564abbfaed10>

3D SDF for #<Metabolite:0x0000564abbfaed10>

3D-SDF for #<Metabolite:0x0000564abbfaed10>

PDB for #<Metabolite:0x0000564abbfaed10>

3D PDB for #<Metabolite:0x0000564abbfaed10>

SMILES for #<Metabolite:0x0000564abbfaed10>

INCHI for #<Metabolite:0x0000564abbfaed10>

Structure for #<Metabolite:0x0000564abbfaed10>

3D Structure for #<Metabolite:0x0000564abbfaed10>