MiMeDB: Showing metabocard for (2R)-2,3-bisphosphoglyceric acid (MMDBc0054827)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:35:46 UTC

Update Date

2022-08-12 20:09:05 UTC

Metabolite ID

MMDBc0054827

Metabolite Identification

Common Name

(2R)-2,3-bisphosphoglyceric acid

Description

(2R)-2,3-bisphosphoglycerate belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group (2R)-2,3-bisphosphoglycerate is a secondary metabolite. Secondary metabolites are metabolically or physiologically non-essential metabolites that may serve a role as defense or signalling molecules. In some cases they are simply molecules that arise from the incomplete metabolism of other secondary metabolites. Based on a literature review very few articles have been published on (2R)-2,3-bisphosphoglycerate.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221352D          

 16 15  0  0  1  0            999 V2000
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.8250   -1.4289    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.0000   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -2.1434    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    4.1250   -1.4289    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.3000   -0.6039    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.3000   -2.2539    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.4289    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -1.4289    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  0  0  0  0
  3  2  1  0  0  0  0
  4  3  2  0  0  0  0
  5  3  1  0  0  0  0
 12  1  1  0  0  0  0
  2 13  1  1  0  0  0
 14  6  1  0  0  0  0
 14  7  1  0  0  0  0
 14  8  2  0  0  0  0
 14 12  1  0  0  0  0
 15  9  1  0  0  0  0
 15 10  1  0  0  0  0
 15 11  2  0  0  0  0
 15 13  1  0  0  0  0
  2 16  1  1  0  0  0
M  CHG  5   5  -1   6  -1   7  -1   9  -1  10  -1
M  END
> <DATABASE_ID>
MMDBc0054827

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C3H8O10P2/c4-3(5)2(13-15(9,10)11)1-12-14(6,7)8/h2H,1H2,(H,4,5)(H2,6,7,8)(H2,9,10,11)/p-5/t2-/m1/s1

> <INCHI_KEY>
XOHUEYCVLUUEJJ-UWTATZPHSA-I

> <FORMULA>
C3H3O10P2

> <MOLECULAR_WEIGHT>
260.997

> <EXACT_MASS>
260.922888192

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
18

> <JCHEM_AVERAGE_POLARIZABILITY>
16.428322164494986

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
0

> <JCHEM_FORMAL_CHARGE>
-5

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R)-2,3-bis(phosphonooxy)propanoate

> <JCHEM_LOGP>
-1.765871547333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-5

> <JCHEM_PKA>
1.2497332376712151

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.4809321990127331

> <JCHEM_POLAR_SURFACE_AREA>
184.97000000000003

> <JCHEM_REFRACTIVITY>
48.47960000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(2R)-2,3-bis(phosphonooxy)propanoate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.540  -2.667   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -0.000  -2.667   0.000  0.00  0.00           O+0
HETATM    5  O   UNK     0       2.310  -4.001   0.000  0.00  0.00           O-1
HETATM    6  O   UNK     0       7.700  -2.667   0.000  0.00  0.00           O-1
HETATM    7  O   UNK     0       6.160  -1.127   0.000  0.00  0.00           O-1
HETATM    8  O   UNK     0       6.160  -4.207   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.540   0.000   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       0.000  -1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       4.620  -2.667   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       6.160  -2.667   0.000  0.00  0.00           P+0
HETATM   15  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   16  H   UNK     0       3.080  -2.667   0.000  0.00  0.00           H+0
CONECT    1    2   12                                                       
CONECT    2    1    3   13   16                                             
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3                                                            
CONECT    6   14                                                            
CONECT    7   14                                                            
CONECT    8   14                                                            
CONECT    9   15                                                            
CONECT   10   15                                                            
CONECT   11   15                                                            
CONECT   12    1   14                                                       
CONECT   13    2   15                                                       
CONECT   14    6    7    8   12                                             
CONECT   15    9   10   11   13                                             
CONECT   16    2                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Value	Source
2,3-Bisphosphonato-D-glycerate	ChEBI
2,3-Bisphosphonato-D-glycerate pentaanion	ChEBI
2,3-Bisphosphonato-D-glyceric acid	Generator
2,3-Bisphosphonato-D-glyceric acid pentaanion	Generator
(2R)-2,3-Bisphosphoglyceric acid	Generator

Molecular Formula

C₃H₃O₁₀P₂

Average Mass

260.997

Monoisotopic Mass

260.922888192

IUPAC Name

(2R)-2,3-bis(phosphonooxy)propanoate

Traditional Name

(2R)-2,3-bis(phosphonooxy)propanoate

CAS Registry Number

Not Available

SMILES

[H][C@](COP([O-])([O-])=O)(OP([O-])([O-])=O)C([O-])=O

InChI Identifier

InChI=1S/C3H8O10P2/c4-3(5)2(13-15(9,10)11)1-12-14(6,7)8/h2H,1H2,(H,4,5)(H2,6,7,8)(H2,9,10,11)/p-5/t2-/m1/s1

InChI Key

XOHUEYCVLUUEJJ-UWTATZPHSA-I

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as sugar acids and derivatives. Sugar acids and derivatives are compounds containing a saccharide unit which bears a carboxylic acid group.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Sugar acids and derivatives

Alternative Parents

Substituents

Glyceric_acid
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Monosaccharide
Monocarboxylic acid or derivatives
Carboxylic acid
Carboxylic acid derivative
Organic oxide
Hydrocarbon derivative
Carbonyl group
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

monocarboxylic acid anion (CHEBI:58248 )
organophosphate oxoanion (CHEBI:58248 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-1.8	ChemAxon
pKa (Strongest Acidic)	0.48	ChemAxon
Physiological Charge	-5	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	0	ChemAxon
Polar Surface Area	184.97 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	48.48 m³·mol⁻¹	ChemAxon
Polarizability	16.43 Å³	ChemAxon
Number of Rings	0	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

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
MMDBr0015851	(2R)-2-phosphoglyceric acid	(2R)-2,3-bisphosphoglyceric acid	2-phosphoglycerate kinase	Phosphorylation	RHEA	34755880
MMDBr0015852	(2R)-2,3-bisphosphoglyceric acid	ADP	Cyclic 2,3-diphosphoglycerate synthetase	Synthesis	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
Archaea/Archaea	Euryarchaeota	16
Archaea	Euryarchaeota	2
Bacteria	Actinobacteria	1

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

26331096

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

25200383

PDB ID

Not Available

ChEBI ID

58248

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

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 (2R)-2,3-bisphosphoglyceric acid (MMDBc0054827)

MOL for #<Metabolite:0x00007fe27ec658f0>

3D MOL for #<Metabolite:0x00007fe27ec658f0>

3D SDF for #<Metabolite:0x00007fe27ec658f0>

3D-SDF for #<Metabolite:0x00007fe27ec658f0>

PDB for #<Metabolite:0x00007fe27ec658f0>

3D PDB for #<Metabolite:0x00007fe27ec658f0>

SMILES for #<Metabolite:0x00007fe27ec658f0>

INCHI for #<Metabolite:0x00007fe27ec658f0>

Structure for #<Metabolite:0x00007fe27ec658f0>

3D Structure for #<Metabolite:0x00007fe27ec658f0>