MiMeDB: Showing metabocard for D-Ribitol 5-phosphate (MMDBc0052982)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-05-16 21:10:55 UTC

Update Date

2022-09-01 02:19:37 UTC

Metabolite ID

MMDBc0052982

Metabolite Identification

Common Name

D-Ribitol 5-phosphate

Description

Structure

MOL SDF PDB SMILES InChI


  Mrv1652304221918532D          

 14 13  0  0  1  0            999 V2000
   -0.1914    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.5230    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.2375   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.9520    1.1270    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    1.9520    1.9520    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.6664    0.7145    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.6664   -0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.3809    1.1270    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.0954    0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.8099    1.1270    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    5.5243    1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.2224    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.3974    1.8414    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  4  1  1  0  0  0
  3  5  1  0  0  0  0
  5  6  1  6  0  0  0
  5  7  1  0  0  0  0
  7  8  1  1  0  0  0
  7  9  1  0  0  0  0
  9 10  1  0  0  0  0
 10 11  1  0  0  0  0
 11 12  1  0  0  0  0
 11 13  1  0  0  0  0
 11 14  2  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0052982

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H13O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3-9H,1-2H2,(H2,10,11,12)/t3-,4+,5-/m0/s1

> <INCHI_KEY>
VJDOAZKNBQCAGE-LMVFSUKVSA-N

> <FORMULA>
C5H13O8P

> <MOLECULAR_WEIGHT>
232.1257

> <EXACT_MASS>
232.034803904

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
27

> <JCHEM_AVERAGE_POLARIZABILITY>
19.080558132314113

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,4S)-2,3,4,5-tetrahydroxypentyl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-2.14

> <JCHEM_LOGP>
-3.2232499379999995

> <ALOGPS_LOGS>
-0.91

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.517789357699702

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4919789137158341

> <JCHEM_PKA_STRONGEST_BASIC>
-2.974203813611499

> <JCHEM_POLAR_SURFACE_AREA>
147.68

> <JCHEM_REFRACTIVITY>
43.314

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
2.85e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
ribitol 5-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 22-APR-19   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   22-APR-19         0                                  
HETATM    1  O   UNK     0      -0.357   1.334   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0       0.976   2.104   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       2.310   1.334   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       2.310  -0.206   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       3.644   2.104   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       3.644   3.644   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       4.977   1.334   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       4.977  -0.206   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       6.311   2.104   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       7.645   1.334   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0       8.978   2.104   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0      10.312   2.874   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       9.748   0.770   0.000  0.00  0.00           O+0
HETATM   14  O   UNK     0       8.208   3.437   0.000  0.00  0.00           O+0
CONECT    1    2                                                            
CONECT    2    1    3                                                       
CONECT    3    2    4    5                                                  
CONECT    4    3                                                            
CONECT    5    3    6    7                                                  
CONECT    6    5                                                            
CONECT    7    5    8    9                                                  
CONECT    8    7                                                            
CONECT    9    7   10                                                       
CONECT   10    9   11                                                       
CONECT   11   10   12   13   14                                             
CONECT   12   11                                                            
CONECT   13   11                                                            
CONECT   14   11                                                            
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
L-Ribitol 1-phosphate	ChEBI
RBT-5-p	ChEBI
Ribitol 5-phosphate	ChEBI
L-Ribitol 1-phosphoric acid	Generator
Ribitol 5-phosphoric acid	Generator
D-Ribitol 5-phosphoric acid	Generator
Ribitol-5-phosphate	MeSH
D-Ribitol-5-phosphoric acid	Generator

Molecular Formula

C₅H₁₃O₈P

Average Mass

232.1257

Monoisotopic Mass

232.034803904

IUPAC Name

{[(2R,3S,4S)-2,3,4,5-tetrahydroxypentyl]oxy}phosphonic acid

Traditional Name

ribitol 5-phosphate

CAS Registry Number

Not Available

SMILES

OC[C@H](O)[C@H](O)[C@H](O)COP(O)(O)=O

InChI Identifier

InChI=1S/C5H13O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3-9H,1-2H2,(H2,10,11,12)/t3-,4+,5-/m0/s1

InChI Key

VJDOAZKNBQCAGE-LMVFSUKVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharide phosphates. These are monosaccharides comprising a phosphated group linked to the carbohydrate unit.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharide phosphates

Alternative Parents

Substituents

Pentose monosaccharide
Monosaccharide phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Secondary alcohol
Polyol
Organic oxide
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ribitol 5-phosphate (CHEBI:16246 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	28.5 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-3.2	ChemAxon
logS	-0.91	ALOGPS
pKa (Strongest Acidic)	1.49	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	147.68 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	43.31 m³·mol⁻¹	ChemAxon
Polarizability	19.08 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	No	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_4_10) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-00lr-3690000000-7623a74c0db37453a86c	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dj-9510000000-ad5c97abd08ecccd0ff0	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-03dj-9200000000-04352b5ec52eb9690b17	2019-02-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-07nl-9320000000-5f76ea229c91d234e70e	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-1e2f9c4466a96bc32d88	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-70a064f10ba7109368d8	2019-02-23	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

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0013119	Cytidine triphosphate	Cytidine diphosphate ribitol	Bifunctional ribulose 5-phosphate reductase/CDP-ribitol pyrophosphorylase Acs1	Transfer of a cytidylyl group	RHEA	34755880
MMDBr0013934	D-Ribitol 5-phosphate	D-Ribulose 5-phosphate	Bifunctional ribulose 5-phosphate reductase/CDP-ribitol pyrophosphorylase Acs1	Reduction	RHEA	34755880
MMDBr0016339	D-Ribitol 5-phosphate	Phosphate	Pdp3-interacting factor 1	Dephosphorylation	RHEA	34755880
MMDBr0016340	D-Ribitol 5-phosphate	Phosphate	Pdp3-interacting factor 1	Dephosphorylation	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
Bacteria	Proteobacteria	2	Human ; Human sputum; Human feces
Bacteria	Firmicutes	32	Human ; Human feces; Cattle
Eukaryota/Fungi	Ascomycota	2
Bacteria	Bacteroidetes	1	Human ; Human feces

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

Not Available

KEGG Compound ID

C01068

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

151104

PDB ID

Not Available

ChEBI ID

16246

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-Ribitol 5-phosphate (MMDBc0052982)

MOL for #<Metabolite:0x00007f5a48093f18>

3D MOL for #<Metabolite:0x00007f5a48093f18>

3D SDF for #<Metabolite:0x00007f5a48093f18>

3D-SDF for #<Metabolite:0x00007f5a48093f18>

PDB for #<Metabolite:0x00007f5a48093f18>

3D PDB for #<Metabolite:0x00007f5a48093f18>

SMILES for #<Metabolite:0x00007f5a48093f18>

INCHI for #<Metabolite:0x00007f5a48093f18>

Structure for #<Metabolite:0x00007f5a48093f18>

3D Structure for #<Metabolite:0x00007f5a48093f18>