MiMeDB: Showing metabocard for (2R)-3-phospho-glyceroyl phosphate (MMDBc0054048)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 22:48:14 UTC

Update Date

2022-09-01 02:26:50 UTC

Metabolite ID

MMDBc0054048

Metabolite Identification

Common Name

(2R)-3-phospho-glyceroyl phosphate

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv1652303231707072D          

 16 15  0  0  1  0            999 V2000
    0.1105   -2.8875    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.1105   -2.0625    0.0000 C   0  0  2  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  5  0  0  0  0  0  0  0  0  0  0
   -0.9059   -4.4270    0.0000 O   0  5  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
    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  5  0  0  0  0  0  0  0  0  0  0
    1.6500   -0.0000    0.0000 O   0  5  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
  2  1  1  1  0  0  0
  2  3  1  6  0  0  0
  2  4  1  0  0  0  0
  4  5  1  0  0  0  0
  5  6  1  0  0  0  0
  6  7  1  0  0  0  0
  6  8  1  0  0  0  0
  6  9  2  0  0  0  0
  2 10  1  0  0  0  0
 10 11  2  0  0  0  0
 10 12  1  0  0  0  0
 12 13  1  0  0  0  0
 13 14  1  0  0  0  0
 13 15  1  0  0  0  0
 13 16  2  0  0  0  0
M  CHG  4   7  -1   8  -1  14  -1  15  -1
M  END
> <DATABASE_ID>
MMDBc0054048

> <DATABASE_NAME>
MIME

> <SMILES>
[H][C@@](O)(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)/p-4/t2-/m1/s1

> <INCHI_KEY>
LJQLQCAXBUHEAZ-UWTATZPHSA-J

> <FORMULA>
C3H4O10P2

> <MOLECULAR_WEIGHT>
262.005

> <EXACT_MASS>
261.930164644

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
19

> <JCHEM_AVERAGE_POLARIZABILITY>
17.00734506719764

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
1

> <JCHEM_FORMAL_CHARGE>
-4

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.25

> <JCHEM_LOGP>
-2.2961706616666664

> <ALOGPS_LOGS>
-0.82

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.6114650905706243

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0092438942915392

> <JCHEM_PKA_STRONGEST_BASIC>
-4.186154544612546

> <JCHEM_POLAR_SURFACE_AREA>
182.14

> <JCHEM_REFRACTIVITY>
37.92930000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
5.02e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R)-2-hydroxy-3-(phosphonooxy)propanoyl]oxyphosphonate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-MAR-17   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-MAR-17         0                                  
HETATM    1  H   UNK     0       0.206  -5.390   0.000  0.00  0.00           H+0
HETATM    2  C   UNK     0       0.206  -3.850   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0       1.540  -4.620   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      -1.127  -4.620   0.000  0.00  0.00           C+0
HETATM    5  O   UNK     0      -1.127  -6.160   0.000  0.00  0.00           O+0
HETATM    6  P   UNK     0      -2.461  -6.930   0.000  0.00  0.00           P+0
HETATM    7  O   UNK     0      -3.795  -7.700   0.000  0.00  0.00           O-1
HETATM    8  O   UNK     0      -1.691  -8.264   0.000  0.00  0.00           O-1
HETATM    9  O   UNK     0      -3.231  -5.596   0.000  0.00  0.00           O+0
HETATM   10  C   UNK     0       0.206  -2.310   0.000  0.00  0.00           C+0
HETATM   11  O   UNK     0      -1.127  -1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.540  -1.540   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0       1.540   0.000   0.000  0.00  0.00           P+0
HETATM   14  O   UNK     0       1.540   1.540   0.000  0.00  0.00           O-1
HETATM   15  O   UNK     0       3.080  -0.000   0.000  0.00  0.00           O-1
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3    4   10                                             
CONECT    3    2                                                            
CONECT    4    2    5                                                       
CONECT    5    4    6                                                       
CONECT    6    5    7    8    9                                             
CONECT    7    6                                                            
CONECT    8    6                                                            
CONECT    9    6                                                            
CONECT   10    2   11   12                                                  
CONECT   11   10                                                            
CONECT   12   10   13                                                       
CONECT   13   12   14   15   16                                             
CONECT   14   13                                                            
CONECT   15   13                                                            
CONECT   16   13                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Value	Source
3-phosphonato-D-Glyceroyl phosphoric acid(4-)	Generator
3-phospho-D-Glyceroyl phosphate	HMDB
3-phospho-D-Glyceroyl phosphoric acid	HMDB
3-phosphonato-D-Glyceroyl phosphate tetraanion	HMDB
3-phosphonato-D-Glyceroyl phosphoric acid tetraanion	HMDB

Molecular Formula

C₃H₄O₁₀P₂

Average Mass

262.005

Monoisotopic Mass

261.930164644

IUPAC Name

{[(2R)-2-hydroxy-3-(phosphonooxy)propanoyl]oxy}phosphonate

Traditional Name

[(2R)-2-hydroxy-3-(phosphonooxy)propanoyl]oxyphosphonate

CAS Registry Number

Not Available

SMILES

[H][C@@](O)(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)/p-4/t2-/m1/s1

InChI Key

LJQLQCAXBUHEAZ-UWTATZPHSA-J

Chemical Taxonomy

Description

This compound 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
Monosaccharide
Alkyl phosphate
Carboxylic acid salt
Secondary alcohol
Monocarboxylic acid or derivatives
Carboxylic acid derivative
Hydrocarbon derivative
Organic oxide
Organooxygen compound
Organic oxygen compound
Alcohol
Carbonyl group
Organic salt
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:57604 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	50.2 g/L	ALOGPS
logP	-1.2	ALOGPS
logP	-2.3	ChemAxon
logS	-0.82	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	1	ChemAxon
Polar Surface Area	182.14 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	37.93 m³·mol⁻¹	ChemAxon
Polarizability	17.01 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
MMDBr0012883	D-Glyceraldehyde 3-phosphate	(2R)-3-phospho-glyceroyl phosphate	Glyceraldehyde-3-phosphate dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0012884	D-Glyceraldehyde 3-phosphate	(2R)-3-phospho-glyceroyl phosphate	Glyceraldehyde-3-phosphate dehydrogenase	Dehydrogenation	RHEA	34755880
MMDBr0012885	D-Glyceraldehyde 3-phosphate	(2R)-3-phospho-glyceroyl phosphate	Glyceraldehyde-3-phosphate dehydrogenase B	Dehydrogenation	RHEA	34755880
MMDBr0013357	(2R)-3-phosphoglyceric acid	(2R)-3-phospho-glyceroyl phosphate	Phosphoglycerate kinase	Phosphorylation	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	Hosts and Body Sites
Archaea/Archaea	Crenarchaeota	16
Archaea/Archaea	Euryarchaeota	34
Archaea/Archaea	nah	3
Archaea	Euryarchaeota	3
Archaea	Crenarchaeota	1
Bacteria	Firmicutes	149	Human feces; Human ; Human subgingival plaque; Human saliva; Catfish ; Cattle
Bacteria	Cyanobacteria	34	Human
Bacteria	nah	1
Eukaryota/Fungi	Ascomycota	41	Human feces
Eukaryota/Fungi	Basidiomycota	15	Human feces
Bacteria	Aquificae	2
Bacteria	Proteobacteria	298	Human ; Human feces; Goat feces; Sheep feces; Human sputum; Human subgingival plaque; Pig ; Cattle ; River trout ; Rat ; Sheep ; Chicken
Bacteria	Bacteroidetes	4	Human ; Human feces
Bacteria	Spirochaetes	18	Human ; Relapsing fever tick
Bacteria	Chlamydiae	9	Human ; Sheep ; Cat
Bacteria	Actinobacteria	61	Human ; Cattle ; Human feces
Bacteria	Tenericutes	11	Human
Bacteria/NULL	Proteobacteria	3	Human ; Human feces; Goat feces; Sheep feces; Human sputum; Human subgingival plaque; Pig ; Cattle ; River trout ; Rat ; Sheep ; Chicken
Eukaryota/Fungi	Mucoromycota	4
Bacteria	Deinococcus-thermus	6
Bacteria	Thermotogae	7
Bacteria	Acidobacteria	3
Bacteria	Verrucomicrobia	1	Human ; Human feces
Bacteria	Chloroflexi	7
Bacteria	Chlorobi	11
Bacteria	Dictyoglomi	2
Bacteria	Elusimicrobia	1
Bacteria	Fusobacteria	1	Human ; Human feces
Bacteria	Planctomycetes	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

HMDB62758

DrugBank ID

Not Available

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

46878409

PDB ID

Not Available

ChEBI ID

57604

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)-3-phospho-glyceroyl phosphate (MMDBc0054048)

MOL for #<Metabolite:0x00007f5a89f9d270>

3D MOL for #<Metabolite:0x00007f5a89f9d270>

3D SDF for #<Metabolite:0x00007f5a89f9d270>

3D-SDF for #<Metabolite:0x00007f5a89f9d270>

PDB for #<Metabolite:0x00007f5a89f9d270>

3D PDB for #<Metabolite:0x00007f5a89f9d270>

SMILES for #<Metabolite:0x00007f5a89f9d270>

INCHI for #<Metabolite:0x00007f5a89f9d270>

Structure for #<Metabolite:0x00007f5a89f9d270>

3D Structure for #<Metabolite:0x00007f5a89f9d270>