MiMeDB: Showing metabocard for Glyceric acid 1,3-biphosphate (MMDBc0029603)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:34:04 UTC

Update Date

2022-08-31 13:58:55 UTC

Metabolite ID

MMDBc0029603

Metabolite Identification

Common Name

Glyceric acid 1,3-biphosphate

Description

1,3-Bisphosphogylcerate (1,3BPG), also known as PGAP, is a 3-carbon organic molecule present in most, if not all living creatures. It primarily exists as a metabolic intermediate in glycolysis during respiration.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652305171801272D          

 15 14  0  0  0  0            999 V2000
    0.1105   -2.0625    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -2.4750    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039   -2.4750    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039   -3.3000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.3184   -3.7125    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0329   -4.1250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -1.2375    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6039   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.9059   -4.4270    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.7309   -2.9980    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    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
  3  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  2  0  0  0  0
  1  7  1  0  0  0  0
  7  8  2  0  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  2  0  0  0  0
 12  5  1  0  0  0  0
 13  5  1  0  0  0  0
 14 10  1  0  0  0  0
 15 10  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0029603

> <DATABASE_NAME>
MIME

> <SMILES>
OC(COP(O)(O)=O)C(=O)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C3H8O10P2/c4-2(1-12-14(6,7)8)3(5)13-15(9,10)11/h2,4H,1H2,(H2,6,7,8)(H2,9,10,11)

> <INCHI_KEY>
LJQLQCAXBUHEAZ-UHFFFAOYSA-N

> <FORMULA>
C3H8O10P2

> <MOLECULAR_WEIGHT>
266.0371

> <EXACT_MASS>
265.9592695

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
18.041428701774514

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[2-hydroxy-3-(phosphonooxy)propanoyl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-1.14

> <JCHEM_LOGP>
-2.2961706616666664

> <ALOGPS_LOGS>
-1.44

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.6114650905706234

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0092438942915383

> <JCHEM_PKA_STRONGEST_BASIC>
-4.186154544612546

> <JCHEM_POLAR_SURFACE_AREA>
170.82

> <JCHEM_REFRACTIVITY>
42.41609999999999

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
9.64e+00 g/l

> <JCHEM_TRADITIONAL_IUPAC>
1,3-bisphosphoglycerate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-MAY-18   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-MAY-18         0                                  
HETATM    1  C   UNK     0       0.206  -3.850   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0       1.540  -4.620   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -1.127  -4.620   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -1.127  -6.160   0.000  0.00  0.00           O+0
HETATM    5  P   UNK     0      -2.461  -6.930   0.000  0.00  0.00           P+0
HETATM    6  O   UNK     0      -3.795  -7.700   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.206  -2.310   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      -1.127  -1.540   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       1.540  -1.540   0.000  0.00  0.00           O+0
HETATM   10  P   UNK     0       1.540   0.000   0.000  0.00  0.00           P+0
HETATM   11  O   UNK     0       1.540   1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -1.691  -8.264   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -3.231  -5.596   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       3.080  -0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2    3    7                                                  
CONECT    2    1                                                            
CONECT    3    1    4                                                       
CONECT    4    3    5                                                       
CONECT    5    4    6   12   13                                             
CONECT    6    5                                                            
CONECT    7    1    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11   14   15                                             
CONECT   11   10                                                            
CONECT   12    5                                                            
CONECT   13    5                                                            
CONECT   14   10                                                            
CONECT   15   10                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

Synonyms

Value	Source
Glycerate 1,3-biphosphate	Generator
Glyceric acid 1,3-biphosphoric acid	Generator
3-Phosphoglyceroyl phosphate	MeSH
1,3-Biphosphoglyceric acid	MeSH
1,3-Bisphosphoglycerate	MeSH
1,3-Diphosphoglycerate	MeSH
1,3-Biphosphoglycerate	HMDB
1,3-Bis-phosphoglycerate	HMDB
1,3-Diphosphateglycerate	HMDB
13-DPG	HMDB
2-Hydroxy-3-(phosphonooxy)-propanoate	HMDB
2-Hydroxy-3-(phosphonooxy)-propanoic acid	HMDB
2-Hydroxy-3-(phosphonooxy)-propanoic acid 1-anhydride with phosphorate	HMDB
2-Hydroxy-3-(phosphonooxy)-propanoic acid 1-anhydride with phosphoric acid	HMDB
3-P-Glyceroyl-P	HMDB
3-phospho-D-Glyceroyl phosphate	HMDB
3-phospho-D-Glyceroyl-phosphate	HMDB
3-Phosphoglyceroyl-P	HMDB
3-Phosphoglyceroyl-phosphate	HMDB
DPG	HMDB
Glycerate 1,3-bisphosphate	HMDB
Glycerate 1,3-diphosphate	HMDB
P-Glyceroyl-P	HMDB
Phosphoglyceroyl-P	HMDB

Molecular Formula

C₃H₈O₁₀P₂

Average Mass

266.0371

Monoisotopic Mass

265.9592695

IUPAC Name

{[2-hydroxy-3-(phosphonooxy)propanoyl]oxy}phosphonic acid

Traditional Name

1,3-bisphosphoglycerate

CAS Registry Number

1981-49-3

SMILES

OC(COP(O)(O)=O)C(=O)OP(O)(O)=O

InChI Identifier

InChI=1S/C3H8O10P2/c4-2(1-12-14(6,7)8)3(5)13-15(9,10)11/h2,4H,1H2,(H2,6,7,8)(H2,9,10,11)

InChI Key

LJQLQCAXBUHEAZ-UHFFFAOYSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as acyl monophosphates. These are organic compounds containing a monophosphate linked to an acyl group. They have the general structure R-CO-P(O)(O)OH, R=H or organyl.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Organic phosphoric acids and derivatives

Sub Class

Phosphate esters

Direct Parent

Acyl monophosphates

Alternative Parents

Substituents

Acyl monophosphate
Glyceric_acid
Monoalkyl phosphate
Monosaccharide
Alkyl phosphate
Carboxylic acid salt
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Organic oxide
Organooxygen compound
Organic oxygen compound
Alcohol
Carbonyl group
Hydrocarbon derivative
Organic salt
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Property	Value	Source
Water Solubility	9.64 g/L	ALOGPS
logP	-1.1	ALOGPS
logP	-2.3	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1.01	ChemAxon
pKa (Strongest Basic)	-4.2	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	170.82 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	42.42 m³·mol⁻¹	ChemAxon
Polarizability	18.04 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

Not Available

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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	174	Human ; Human feces; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	369	Pig ; Human feces; Human ; Human pleural fluid plaque; Cattle	Metabolic reconstruction
Bacteria	Actinobacteria	119	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human nasopharyngeal swab	Metabolic reconstruction
Bacteria	Bacteroidetes	116	Human feces; Human appendix biopsy; Human	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Synergistetes	3	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	5	Human feces; Cattle ; Human	Metabolic reconstruction
Bacteria	Fusobacteria	19	Human ; Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1	Human feces	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Tenericutes	4	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1	Human feces	Unknown

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

HMDB0062758

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022524

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

683

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 ]

Showing metabocard for Glyceric acid 1,3-biphosphate (MMDBc0029603)

MOL for #<Metabolite:0x00007f121800c900>

3D MOL for #<Metabolite:0x00007f121800c900>

3D SDF for #<Metabolite:0x00007f121800c900>

3D-SDF for #<Metabolite:0x00007f121800c900>

PDB for #<Metabolite:0x00007f121800c900>

3D PDB for #<Metabolite:0x00007f121800c900>

SMILES for #<Metabolite:0x00007f121800c900>

INCHI for #<Metabolite:0x00007f121800c900>

Structure for #<Metabolite:0x00007f121800c900>

3D Structure for #<Metabolite:0x00007f121800c900>