MiMeDB: Showing metabocard for L-ribulose 5-phosphate (MMDBc0032117)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 02:03:07 UTC

Update Date

2022-08-31 18:30:41 UTC

Metabolite ID

MMDBc0032117

Metabolite Identification

Common Name

L-ribulose 5-phosphate

Description

L-Ribulose 5-phosphate is a member of the chemical class known as Pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. In Escherichia coli, RpiA catalyzes the interconversion of ribose-5-phosphate and ribulose-5-phosphate and is a key enzyme in the pentose phosphate pathway. (PMID 12182339 ) Interconversion of D-ribose-5-phosphate (R5P) and D-ribulose-5-phosphate is an important step in the pentose phosphate pathway. (PMID 18640127 ) A key player in LPS synthesis is the enzyme D-arabinose-5-phosphate isomerase (API), which catalyzes the reversible isomerization of D-ribulose-5-phosphate to D-arabinose-5-phosphate, a precursor of 3-deoxy-D-manno-octulosonate that is an essential residue of the LPS inner core. (PMID 20954237 ) Dihydroxybutanone phosphate synthase (DS) catalyzes a commitment step in riboflavin biosynthesis where ribulose 5-phosphate is converted to dihydroxybutanone phosphate and formate. (PMID 11053863 ) Ribose-5-phosphate isomerase A (RpiA) plays an important role in interconverting between ribose-5-phosphate (R5P) and ribulose-5-phosphate in the pentose phosphate pathway and the Calvin cycle. (PMID 19214439 )

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 04061520222D          

 14 13  0  0  0  0            999 V2000
   -2.8578   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1434    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4289   -1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7144    0.2062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.7144    1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.2062    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.0000   -1.0312    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7144    0.2062    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.4289   -0.2062    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.1434    0.2062    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.8578    0.6187    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    2.5559   -0.5082    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    1.7309    0.9207    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  2  0  0  0  0
  3  5  1  0  0  0  0
  5  6  1  1  0  0  0
  5  7  1  0  0  0  0
  7  8  1  6  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  CHG  2  12  -1  13  -1
M  END
> <DATABASE_ID>
MMDBc0032117

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/p-2/t4-,5+/m0/s1

> <INCHI_KEY>
FNZLKVNUWIIPSJ-CRCLSJGQSA-L

> <FORMULA>
C5H9O8P

> <MOLECULAR_WEIGHT>
228.094

> <EXACT_MASS>
228.004601408

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_ATOM_COUNT>
23

> <JCHEM_AVERAGE_POLARIZABILITY>
17.58827706808278

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3S,4S)-1,3,4-trihydroxy-5-(phosphonatooxy)pentan-2-one

> <ALOGPS_LOGP>
-1.86

> <JCHEM_LOGP>
-2.7602629813333333

> <ALOGPS_LOGS>
-0.63

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.504370847667953

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4785529591465414

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3276267100529333

> <JCHEM_POLAR_SURFACE_AREA>
150.18

> <JCHEM_REFRACTIVITY>
40.2288

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
6.23e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-ribulose 5-phosphate(2-)

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 06-APR-15   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   06-APR-15         0                                  
HETATM    1  O   UNK     0      -5.335  -0.385   0.000  0.00  0.00           O+0
HETATM    2  C   UNK     0      -4.001   0.385   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -2.667  -0.385   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      -2.667  -1.925   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -1.334   0.385   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -1.334   1.925   0.000  0.00  0.00           O+0
HETATM    7  C   UNK     0       0.000  -0.385   0.000  0.00  0.00           C+0
HETATM    8  O   UNK     0       0.000  -1.925   0.000  0.00  0.00           O+0
HETATM    9  C   UNK     0       1.334   0.385   0.000  0.00  0.00           C+0
HETATM   10  O   UNK     0       2.667  -0.385   0.000  0.00  0.00           O+0
HETATM   11  P   UNK     0       4.001   0.385   0.000  0.00  0.00           P+0
HETATM   12  O   UNK     0       5.335   1.155   0.000  0.00  0.00           O-1
HETATM   13  O   UNK     0       4.771  -0.949   0.000  0.00  0.00           O-1
HETATM   14  O   UNK     0       3.231   1.719   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
5-O-Phosphonato-L-erythro-pent-2-ulose	ChEBI
5-O-Phosphonato-L-ribulose	ChEBI
L-Ribulose 5-phosphate	ChEBI
L-Ribulose 5-phosphate dianion	ChEBI
L-Ribulose 5-phosphoric acid	Generator
L-Ribulose 5-phosphoric acid dianion	Generator
L-Ribulose 5-phosphoric acid	Generator

Molecular Formula

C₅H₉O₈P

Average Mass

228.094

Monoisotopic Mass

228.004601408

IUPAC Name

(3S,4S)-1,3,4-trihydroxy-5-(phosphonatooxy)pentan-2-one

Traditional Name

L-ribulose 5-phosphate(2-)

CAS Registry Number

Not Available

SMILES

OCC(=O)[C@@H](O)[C@@H](O)COP([O-])([O-])=O

InChI Identifier

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h4-6,8-9H,1-2H2,(H2,10,11,12)/p-2/t4-,5+/m0/s1

InChI Key

FNZLKVNUWIIPSJ-CRCLSJGQSA-L

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
Acyloin
Beta-hydroxy ketone
Organic phosphoric acid derivative
Phosphoric acid ester
Alkyl phosphate
Alpha-hydroxy ketone
Ketone
Secondary alcohol
Polyol
Hydrocarbon derivative
Organic oxide
Carbonyl group
Primary alcohol
Alcohol
Organic anion
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

organophosphate oxoanion (CHEBI:58226 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	62.3 g/L	ALOGPS
logP	-1.9	ALOGPS
logP	-2.8	ChemAxon
logS	-0.63	ALOGPS
pKa (Strongest Acidic)	1.48	ChemAxon
pKa (Strongest Basic)	-3.3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	7	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	150.18 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	40.23 m³·mol⁻¹	ChemAxon
Polarizability	17.59 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

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0018152	L-ribulose 5-phosphate	Xylulose 5-phosphate	L-ribulose-5-phosphate 4-epimerase UlaF	Epimerization	PathBank	31602464
MMDBr0018154	L-Xylulose 5-phosphate	L-ribulose 5-phosphate	L-ribulose-5-phosphate 3-epimerase UlaE	Epimerization	PathBank	31602464
MMDBr0018156	L-ribulose 5-phosphate	Xylulose 5-phosphate	L-ribulose-5-phosphate 4-epimerase SgbE	Epimerization	PathBank	31602464
MMDBr0019368	L-Xylulose 5-phosphate	L-ribulose 5-phosphate	Putative L-ribulose-5-phosphate 3-epimerase SgbU	Epimerization	PathBank	31602464
MMDBr0019369	L-ribulose 5-phosphate	Xylulose 5-phosphate	L-ribulose-5-phosphate 4-epimerase UlaF	Epimerization	PathBank	31602464
MMDBr0019371	L-Ribulose	L-ribulose 5-phosphate	Ribulokinase	Phosphorylation	PathBank	31602464

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

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

21145006

PDB ID

Not Available

ChEBI ID

58226

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 ]

Showing metabocard for L-ribulose 5-phosphate (MMDBc0032117)

MOL for #<Metabolite:0x00007f9238636d80>

3D MOL for #<Metabolite:0x00007f9238636d80>

3D SDF for #<Metabolite:0x00007f9238636d80>

3D-SDF for #<Metabolite:0x00007f9238636d80>

PDB for #<Metabolite:0x00007f9238636d80>

3D PDB for #<Metabolite:0x00007f9238636d80>

SMILES for #<Metabolite:0x00007f9238636d80>

INCHI for #<Metabolite:0x00007f9238636d80>

Structure for #<Metabolite:0x00007f9238636d80>

3D Structure for #<Metabolite:0x00007f9238636d80>