MiMeDB: Showing metabocard for D-ribose 5-triphosphate (MMDBc0055875)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-17 20:09:33 UTC

Update Date

2022-08-12 20:09:28 UTC

Metabolite ID

MMDBc0055875

Metabolite Identification

Common Name

D-ribose 5-triphosphate

Description

D-ribose 5-triphosphate(4-), also known as D-ribose 5-triphosphoric acid, 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. Based on a literature review a significant number of articles have been published on D-ribose 5-triphosphate(4-).

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172222092D          

 26 26  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
   -0.8843    0.8843    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
    6.9976    0.2480    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.4679   -0.7916    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.9580    0.7776    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6725   -0.1974    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.1626    1.3718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2632   -0.3230    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3673    0.9032    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
    5.4283   -0.2619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2022    0.8421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2130   -0.0070    0.0000 P   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
    4.8153    0.2901    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
  4  7  1  6  0  0  0
  8  5  1  0  0  0  0
 16  1  1  0  0  0  0
 17  2  1  0  0  0  0
 17  5  1  0  0  0  0
 20  9  1  0  0  0  0
 20 10  1  0  0  0  0
 20 11  2  0  0  0  0
 20 18  1  0  0  0  0
 21 12  1  0  0  0  0
 21 13  2  0  0  0  0
 21 16  1  0  0  0  0
 21 19  1  0  0  0  0
 22 14  1  0  0  0  0
 22 15  2  0  0  0  0
 22 18  1  0  0  0  0
 22 19  1  0  0  0  0
  2 23  1  6  0  0  0
  3 24  1  1  0  0  0
  4 25  1  1  0  0  0
 26  5  1  0  0  0  0
M  CHG  4   9  -1  10  -1  12  -1  14  -1
M  END


  Mrv1652306172222092D          

 26 26  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
   -0.8843    0.8843    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
    6.9976    0.2480    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    6.4679   -0.7916    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.9580    0.7776    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.6725   -0.1974    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    3.1626    1.3718    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2632   -0.3230    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    5.3673    0.9032    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
    5.4283   -0.2619    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2022    0.8421    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    6.2130   -0.0070    0.0000 P   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
    4.8153    0.2901    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
  4  7  1  6  0  0  0
  8  5  1  0  0  0  0
 16  1  1  0  0  0  0
 17  2  1  0  0  0  0
 17  5  1  0  0  0  0
 20  9  1  0  0  0  0
 20 10  1  0  0  0  0
 20 11  2  0  0  0  0
 20 18  1  0  0  0  0
 21 12  1  0  0  0  0
 21 13  2  0  0  0  0
 21 16  1  0  0  0  0
 21 19  1  0  0  0  0
 22 14  1  0  0  0  0
 22 15  2  0  0  0  0
 22 18  1  0  0  0  0
 22 19  1  0  0  0  0
  2 23  1  6  0  0  0
  3 24  1  1  0  0  0
  4 25  1  1  0  0  0
 26  5  1  0  0  0  0
M  CHG  4   9  -1  10  -1  12  -1  14  -1
M  END
> <DATABASE_ID>
MMDBc0055875

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H13O14P3/c6-3-2(17-5(8)4(3)7)1-16-21(12,13)19-22(14,15)18-20(9,10)11/h2-8H,1H2,(H,12,13)(H,14,15)(H2,9,10,11)/p-4/t2-,3-,4-,5?/m1/s1

> <INCHI_KEY>
ZJJBHGDNOZLBIL-SOOFDHNKSA-J

> <FORMULA>
C5H9O14P3

> <MOLECULAR_WEIGHT>
386.036

> <EXACT_MASS>
385.922710283

> <JCHEM_ACCEPTOR_COUNT>
11

> <JCHEM_ATOM_COUNT>
31

> <JCHEM_AVERAGE_POLARIZABILITY>
26.087342343612267

> <JCHEM_BIOAVAILABILITY>
0

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-4

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(phosphonooxy)({[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methyl phosphono}oxy)phosphinate

> <JCHEM_LOGP>
-3.269367265333333

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-3

> <JCHEM_PKA>
2.5314733923024346

> <JCHEM_PKA_STRONGEST_ACIDIC>
0.8952809846251513

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6800847325926993

> <JCHEM_POLAR_SURFACE_AREA>
241.05999999999995

> <JCHEM_REFRACTIVITY>
58.09280000000001

> <JCHEM_ROTATABLE_BOND_COUNT>
7

> <JCHEM_RULE_OF_FIVE>
0

> <JCHEM_TRADITIONAL_IUPAC>
phosphonooxy({[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methyl phosphono}oxy)phosphinate

> <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      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      13.062   0.463   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0      12.073  -1.478   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0      11.122   1.452   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       6.855  -0.369   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0       5.904   2.561   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       7.958  -0.603   0.000  0.00  0.00           O-1
HETATM   15  O   UNK     0      10.019   1.686   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       4.915   0.620   0.000  0.00  0.00           O+0
HETATM   17  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM   18  O   UNK     0      10.133  -0.489   0.000  0.00  0.00           O+0
HETATM   19  O   UNK     0       7.844   1.572   0.000  0.00  0.00           O+0
HETATM   20  P   UNK     0      11.598  -0.013   0.000  0.00  0.00           P+0
HETATM   21  P   UNK     0       6.379   1.096   0.000  0.00  0.00           P+0
HETATM   22  P   UNK     0       8.988   0.542   0.000  0.00  0.00           P+0
HETATM   23  H   UNK     0       2.547   2.696   0.000  0.00  0.00           H+0
HETATM   24  H   UNK     0      -0.312   2.779   0.000  0.00  0.00           H+0
HETATM   25  H   UNK     0      -1.275   0.086   0.000  0.00  0.00           H+0
HETATM   26  H   UNK     0       0.989  -1.662   0.000  0.00  0.00           H+0
CONECT    1    2   16                                                       
CONECT    2    1    3   17   23                                             
CONECT    3    2    4    6   24                                             
CONECT    4    3    5    7   25                                             
CONECT    5    4    8   17   26                                             
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9   20                                                            
CONECT   10   20                                                            
CONECT   11   20                                                            
CONECT   12   21                                                            
CONECT   13   21                                                            
CONECT   14   22                                                            
CONECT   15   22                                                            
CONECT   16    1   21                                                       
CONECT   17    2    5                                                       
CONECT   18   20   22                                                       
CONECT   19   21   22                                                       
CONECT   20    9   10   11   18                                             
CONECT   21   12   13   16   19                                             
CONECT   22   14   15   18   19                                             
CONECT   23    2                                                            
CONECT   24    3                                                            
CONECT   25    4                                                            
CONECT   26    5                                                            
MASTER        0    0    0    0    0    0    0    0   26    0   52    0
END

Synonyms

Value	Source
D-Ribose 5-triphosphate	ChEBI
D-Ribose 5-triphosphoric acid	Generator
D-Ribose 5-triphosphoric acid(4-)	Generator

Molecular Formula

C₅H₉O₁₄P₃

Average Mass

386.036

Monoisotopic Mass

385.922710283

IUPAC Name

(phosphonooxy)({[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methyl phosphono}oxy)phosphinate

Traditional Name

phosphonooxy({[(2R,3S,4R)-3,4,5-trihydroxyoxolan-2-yl]methyl phosphono}oxy)phosphinate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H13O14P3/c6-3-2(17-5(8)4(3)7)1-16-21(12,13)19-22(14,15)18-20(9,10)11/h2-8H,1H2,(H,12,13)(H,14,15)(H2,9,10,11)/p-4/t2-,3-,4-,5?/m1/s1

InChI Key

ZJJBHGDNOZLBIL-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
Alkyl phosphate
Phosphoric acid ester
Tetrahydrofuran
1,2-diol
Hemiacetal
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Polyol
Organic oxide
Hydrocarbon derivative
Alcohol
Organic anion
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
logP	-3.3	ChemAxon
pKa (Strongest Acidic)	0.9	ChemAxon
pKa (Strongest Basic)	-3.7	ChemAxon
Physiological Charge	-3	ChemAxon
Hydrogen Acceptor Count	11	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	241.06 Å²	ChemAxon
Rotatable Bond Count	7	ChemAxon
Refractivity	58.09 m³·mol⁻¹	ChemAxon
Polarizability	26.09 Å³	ChemAxon
Number of Rings	1	ChemAxon
Bioavailability	No	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Deposition Date	View
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	View Spectrum

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

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	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

58145849

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

118796930

PDB ID

Not Available

ChEBI ID

91013

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 D-ribose 5-triphosphate (MMDBc0055875)

MOL for #<Metabolite:0x00005634c277b440>

3D MOL for #<Metabolite:0x00005634c277b440>

3D SDF for #<Metabolite:0x00005634c277b440>

3D-SDF for #<Metabolite:0x00005634c277b440>

PDB for #<Metabolite:0x00005634c277b440>

3D PDB for #<Metabolite:0x00005634c277b440>

SMILES for #<Metabolite:0x00005634c277b440>

INCHI for #<Metabolite:0x00005634c277b440>

Structure for #<Metabolite:0x00005634c277b440>

3D Structure for #<Metabolite:0x00005634c277b440>