MiMeDB: Showing metabocard for D-ribose 2,5-bisphosphate (MMDBc0055874)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:09:32 UTC

Update Date

2025-10-07 16:09:26 UTC

Metabolite ID

MMDBc0055874

Metabolite Identification

Common Name

D-ribose 2,5-bisphosphate

Description

D-ribose 2,5-bisphosphate is a nucleotide sugar phosphate belonging to the class of ribonucleotides. There is limited literature available on this metabolite, indicating that further research may be necessary to fully understand its biological significance and functions.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222092D          

 22 22  0  0  1  0            999 V2000
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2022    0.8421    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.1626    1.3718    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.6725   -0.1974    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1105   -0.2198    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -2.0494    0.9454    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
   -0.9454   -0.2808    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6329    0.3323    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.4175    0.5872    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4974    0.3323    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.3643    1.4442    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1673    1.4888    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
   -0.6830    0.0460    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.5298   -0.8903    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  3  6  1  6  0  0  0
  7  5  1  0  0  0  0
 14  1  1  0  0  0  0
 15  2  1  0  0  0  0
 15  5  1  0  0  0  0
  4 16  1  6  0  0  0
 17  8  1  0  0  0  0
 17  9  1  0  0  0  0
 17 10  2  0  0  0  0
 17 14  1  0  0  0  0
 18 11  1  0  0  0  0
 18 12  1  0  0  0  0
 18 13  2  0  0  0  0
 18 16  1  0  0  0  0
  2 19  1  6  0  0  0
  3 20  1  1  0  0  0
  4 21  1  1  0  0  0
 22  5  1  0  0  0  0
M  CHG  4   8  -1   9  -1  11  -1  12  -1
M  END
> <DATABASE_ID>
MMDBc0055874

> <DATABASE_NAME>
MIME

> <SMILES>
[H]C1(O)O[C@]([H])(COP([O-])([O-])=O)[C@@]([H])(O)[C@@]1([H])OP([O-])([O-])=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O11P2/c6-3-2(1-14-17(8,9)10)15-5(7)4(3)16-18(11,12)13/h2-7H,1H2,(H2,8,9,10)(H2,11,12,13)/p-4/t2-,3-,4-,5?/m1/s1

> <INCHI_KEY>
IPSYCGBKVMUNSL-SOOFDHNKSA-J

> <FORMULA>
C5H8O11P2

> <MOLECULAR_WEIGHT>
306.058

> <EXACT_MASS>
305.956379393

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_ATOM_COUNT>
26

> <JCHEM_AVERAGE_POLARIZABILITY>
21.569483508543094

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-4

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4R,5R)-2,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-3-yl phosphate

> <JCHEM_LOGP>
-2.5493363386666665

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.3408936794124253

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.599791414061067

> <JCHEM_PKA_STRONGEST_BASIC>
-3.701298576539762

> <JCHEM_POLAR_SURFACE_AREA>
194.53

> <JCHEM_REFRACTIVITY>
47.2199

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4R,5R)-2,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-3-yl phosphate

> <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       3.770   1.651   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       7.844   1.572   0.000  0.00  0.00           O-1
HETATM    9  O   UNK     0       5.904   2.561   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0       6.855  -0.369   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      -3.940  -0.410   0.000  0.00  0.00           O-1
HETATM   12  O   UNK     0      -3.826   1.765   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0      -1.765  -0.524   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       4.915   0.620   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM   17  P   UNK     0       6.379   1.096   0.000  0.00  0.00           P+0
HETATM   18  P   UNK     0      -2.795   0.620   0.000  0.00  0.00           P+0
HETATM   19  H   UNK     0       2.547   2.696   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0      -0.312   2.779   0.000  0.00  0.00           H+0
HETATM   21  H   UNK     0      -1.275   0.086   0.000  0.00  0.00           H+0
HETATM   22  H   UNK     0       0.989  -1.662   0.000  0.00  0.00           H+0
CONECT    1    2   14                                                       
CONECT    2    1    3   15   19                                             
CONECT    3    2    4    6   20                                             
CONECT    4    3    5   16   21                                             
CONECT    5    4    7   15   22                                             
CONECT    6    3                                                            
CONECT    7    5                                                            
CONECT    8   17                                                            
CONECT    9   17                                                            
CONECT   10   17                                                            
CONECT   11   18                                                            
CONECT   12   18                                                            
CONECT   13   18                                                            
CONECT   14    1   17                                                       
CONECT   15    2    5                                                       
CONECT   16    4   18                                                       
CONECT   17    8    9   10   14                                             
CONECT   18   11   12   13   16                                             
CONECT   19    2                                                            
CONECT   20    3                                                            
CONECT   21    4                                                            
CONECT   22    5                                                            
MASTER        0    0    0    0    0    0    0    0   22    0   44    0
END

Synonyms

Value	Source
D-Ribose 2,5-bisphosphoric acid	Generator

Molecular Formula

C₅H₈O₁₁P₂

Average Mass

306.058

Monoisotopic Mass

305.956379393

IUPAC Name

(3R,4R,5R)-2,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-3-yl phosphate

Traditional Name

(3R,4R,5R)-2,4-dihydroxy-5-[(phosphonooxy)methyl]oxolan-3-yl phosphate

CAS Registry Number

Not Available

SMILES

[H]C1(O)O[C@]([H])(COP([O-])([O-])=O)[C@@]([H])(O)[C@@]1([H])OP([O-])([O-])=O

InChI Identifier

InChI=1S/C5H12O11P2/c6-3-2(1-14-17(8,9)10)15-5(7)4(3)16-18(11,12)13/h2-7H,1H2,(H2,8,9,10)(H2,11,12,13)/p-4/t2-,3-,4-,5?/m1/s1

InChI Key

IPSYCGBKVMUNSL-SOOFDHNKSA-J

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
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Tetrahydrofuran
Hemiacetal
Secondary alcohol
Organoheterocyclic compound
Oxacycle
Hydrocarbon derivative
Organic oxide
Alcohol
Organic anion
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:78345 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-2.5	ChemAxon
pKa (Strongest Acidic)	0.6	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	194.53 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	47.22 m³·mol⁻¹	ChemAxon
Polarizability	21.57 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

Chromatographic Retention Times and Retention Indices

Retention Times

Not Available

Retention Indices

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

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/Eubacteria	Actinobacteria	1	Human ; Human feces

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

31150544

KEGG Compound ID

Not Available

BioCyc ID

CPD-15894

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

86289534

PDB ID

Not Available

ChEBI ID

78345

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 D-ribose 2,5-bisphosphate (MMDBc0055874)

MOL for #<Metabolite:0x00007fadc71eb0a0>

3D MOL for #<Metabolite:0x00007fadc71eb0a0>

3D SDF for #<Metabolite:0x00007fadc71eb0a0>

3D-SDF for #<Metabolite:0x00007fadc71eb0a0>

PDB for #<Metabolite:0x00007fadc71eb0a0>

3D PDB for #<Metabolite:0x00007fadc71eb0a0>

SMILES for #<Metabolite:0x00007fadc71eb0a0>

INCHI for #<Metabolite:0x00007fadc71eb0a0>

Structure for #<Metabolite:0x00007fadc71eb0a0>

3D Structure for #<Metabolite:0x00007fadc71eb0a0>