MiMeDB: Showing metabocard for alpha-D-Ribose 1-methylphosphonate 5-phosphate (MMDBc0031931)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:55:30 UTC

Update Date

2022-08-31 18:26:32 UTC

Metabolite ID

MMDBc0031931

Metabolite Identification

Common Name

alpha-D-Ribose 1-methylphosphonate 5-phosphate

Description

An organophosphate oxoanion obtained by deprotonation of the phosphate and phosphonate OH groups of Œ±-D-ribose 1-methylphosphonate 5-phosphate; major species at pH 7.3.

Structure

MOL SDF PDB SMILES InChI

 
  Mrv1533006051502352D          
 
 18 18  0  0  1  0            999 V2000
   14.5174   -9.0661    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.7516   -9.5635    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   13.0730   -9.0553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.4942  -10.3081    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.4118   -9.5286    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   12.6693  -10.3081    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   11.6253   -9.2746    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   11.0093   -9.8314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1741   -9.8314    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    9.3424   -9.8314    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1707  -10.6631    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.1707   -8.9996    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2086   -9.1065    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   15.3818   -9.0996    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   15.3818   -9.9230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.3818   -8.2692    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.9731  -10.9801    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.1880  -10.9738    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  6  0  0  0
  2  3  1  0  0  0  0
  2  4  1  0  0  0  0
  3  5  1  0  0  0  0
  4  6  1  0  0  0  0
  5  7  1  1  0  0  0
  7  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 10  1  0  0  0  0
  9 11  1  0  0  0  0
  9 12  2  0  0  0  0
  5  6  1  0  0  0  0
 13 14  1  0  0  0  0
 14 15  1  0  0  0  0
 14 16  2  0  0  0  0
  1 14  1  0  0  0  0
  4 17  1  6  0  0  0
  6 18  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031931

> <DATABASE_NAME>
MIME

> <SMILES>
CP(O)(=O)O[C@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

> <INCHI_IDENTIFIER>
InChI=1S/C6H14O10P2/c1-17(9,10)16-6-5(8)4(7)3(15-6)2-14-18(11,12)13/h3-8H,2H2,1H3,(H,9,10)(H2,11,12,13)/t3-,4-,5-,6-/m1/s1

> <INCHI_KEY>
RITBIFGLPRFTSB-KVTDHHQDSA-N

> <FORMULA>
C6H14O10P2

> <MOLECULAR_WEIGHT>
308.116

> <EXACT_MASS>
308.006220647

> <JCHEM_ACCEPTOR_COUNT>
8

> <JCHEM_ATOM_COUNT>
32

> <JCHEM_AVERAGE_POLARIZABILITY>
23.926262327896

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4R,5R)-3,4-dihydroxy-5-{[hydroxy(methyl)phosphoryl]oxy}oxolan-2-yl]methoxy}phosphonic acid

> <ALOGPS_LOGP>
-1.45

> <JCHEM_LOGP>
-2.6977081359999993

> <ALOGPS_LOGS>
-1.20

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
1.5709245679146573

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.9641441996735907

> <JCHEM_PKA_STRONGEST_BASIC>
-3.680853315983626

> <JCHEM_POLAR_SURFACE_AREA>
162.98

> <JCHEM_REFRACTIVITY>
54.2328

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
1.92e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(2R,3S,4R,5R)-3,4-dihydroxy-5-{[hydroxy(methyl)phosphoryl]oxy}oxolan-2-yl]methoxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 05-JUN-15   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   05-JUN-15         0                                  
HETATM    1  O   UNK     0      27.099 -16.923   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      25.670 -17.852   0.000  0.00  0.00           C+0
HETATM    3  O   UNK     0      24.403 -16.903   0.000  0.00  0.00           O+0
HETATM    4  C   UNK     0      25.189 -19.242   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      23.169 -17.787   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      23.649 -19.242   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0      21.701 -17.313   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0      20.551 -18.352   0.000  0.00  0.00           O+0
HETATM    9  P   UNK     0      18.992 -18.352   0.000  0.00  0.00           P+0
HETATM   10  O   UNK     0      17.439 -18.352   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      18.985 -19.905   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      18.985 -16.799   0.000  0.00  0.00           O+0
HETATM   13  C   UNK     0      30.256 -16.999   0.000  0.00  0.00           C+0
HETATM   14  P   UNK     0      28.713 -16.986   0.000  0.00  0.00           P+0
HETATM   15  O   UNK     0      28.713 -18.523   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      28.713 -15.436   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0      26.083 -20.496   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      22.751 -20.484   0.000  0.00  0.00           O+0
CONECT    1    2   14                                                       
CONECT    2    1    3    4                                                  
CONECT    3    2    5                                                       
CONECT    4    2    6   17                                                  
CONECT    5    3    7    6                                                  
CONECT    6    4    5   18                                                  
CONECT    7    5    8                                                       
CONECT    8    7    9                                                       
CONECT    9    8   10   11   12                                             
CONECT   10    9                                                            
CONECT   11    9                                                            
CONECT   12    9                                                            
CONECT   13   14                                                            
CONECT   14   13   15   16    1                                             
CONECT   15   14                                                            
CONECT   16   14                                                            
CONECT   17    4                                                            
CONECT   18    6                                                            
MASTER        0    0    0    0    0    0    0    0   18    0   36    0
END

Synonyms

Value	Source
a-D-Ribose 1-methylphosphonate 5-phosphate	Generator
a-D-Ribose 1-methylphosphonic acid 5-phosphoric acid	Generator
alpha-D-Ribose 1-methylphosphonic acid 5-phosphoric acid	Generator
Α-D-ribose 1-methylphosphonate 5-phosphate	Generator
Α-D-ribose 1-methylphosphonic acid 5-phosphoric acid	Generator

Molecular Formula

C₆H₁₄O₁₀P₂

Average Mass

308.116

Monoisotopic Mass

308.006220647

IUPAC Name

{[(2R,3S,4R,5R)-3,4-dihydroxy-5-{[hydroxy(methyl)phosphoryl]oxy}oxolan-2-yl]methoxy}phosphonic acid

Traditional Name

[(2R,3S,4R,5R)-3,4-dihydroxy-5-{[hydroxy(methyl)phosphoryl]oxy}oxolan-2-yl]methoxyphosphonic acid

CAS Registry Number

Not Available

SMILES

CP(O)(=O)O[C@H]1O[C@H](COP(O)(O)=O)[C@@H](O)[C@H]1O

InChI Identifier

InChI=1S/C6H14O10P2/c1-17(9,10)16-6-5(8)4(7)3(15-6)2-14-18(11,12)13/h3-8H,2H2,1H3,(H,9,10)(H2,11,12,13)/t3-,4-,5-,6-/m1/s1

InChI Key

RITBIFGLPRFTSB-KVTDHHQDSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentose phosphates. These are carbohydrate derivatives containing a pentose substituted by one or more phosphate groups.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentose phosphates

Alternative Parents

Substituents

Pentose phosphate
Pentose-5-phosphate
Monosaccharide phosphate
Monoalkyl phosphate
Organic phosphoric acid derivative
Phosphoric acid ester
Phosphonic acid ester
Alkyl phosphate
Organophosphonic acid derivative
Organophosphonic acid
Tetrahydrofuran
Secondary alcohol
1,2-diol
Oxacycle
Organoheterocyclic compound
Alcohol
Hydrocarbon derivative
Organic oxide
Organophosphorus compound
Organopnictogen compound
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

ribose monophosphate (CHEBI:68820 )
organic phosphonate (CHEBI:68820 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	19.2 g/L	ALOGPS
logP	-1.4	ALOGPS
logP	-2.7	ChemAxon
logS	-1.2	ALOGPS
pKa (Strongest Acidic)	0.96	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	8	ChemAxon
Hydrogen Donor Count	5	ChemAxon
Polar Surface Area	162.98 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	54.23 m³·mol⁻¹	ChemAxon
Polarizability	23.93 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

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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0019290	alpha-D-Ribose 1-methylphosphonate 5-triphosphate	alpha-D-Ribose 1-methylphosphonate 5-phosphate	Alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase	Dephosphorylation	PathBank	31602464
MMDBr0019291	alpha-D-Ribose 1-methylphosphonate 5-phosphate	Methane	Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase	Non-hydrolytic bond cleavage (or its reversal)	PathBank	31602464
MMDBr0024932	S-Adenosylmethionine	Methane	Alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase	Non-hydrolytic bond cleavage (or its reversal)	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	Microbial Links
Bacteria/Eubacteria	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	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

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

Not Available

KEGG Compound ID

C20423

BioCyc ID

CPD0-2480

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

70678985

PDB ID

Not Available

ChEBI ID

68820

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 alpha-D-Ribose 1-methylphosphonate 5-phosphate (MMDBc0031931)

MOL for #<Metabolite:0x00007f9221229448>

3D MOL for #<Metabolite:0x00007f9221229448>

3D SDF for #<Metabolite:0x00007f9221229448>

3D-SDF for #<Metabolite:0x00007f9221229448>

PDB for #<Metabolite:0x00007f9221229448>

3D PDB for #<Metabolite:0x00007f9221229448>

SMILES for #<Metabolite:0x00007f9221229448>

INCHI for #<Metabolite:0x00007f9221229448>

Structure for #<Metabolite:0x00007f9221229448>

3D Structure for #<Metabolite:0x00007f9221229448>