MiMeDB: Showing metabocard for L-Ribulose 5-phosphate (MMDBc0030075)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:52:57 UTC

Update Date

2022-08-31 17:39:31 UTC

Metabolite ID

MMDBc0030075

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 08131209302D          

 16 15  0  0  0  0            999 V2000
   -1.1270   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.7309   -0.3020    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -0.7145    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -1.8414   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.4125   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164   -1.5395    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020    0.5230    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.8743    0.1105    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5724   -1.0164    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.7474    0.4125    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4454   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.1599   -0.3020    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    1.0164    0.1105    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    0.3020   -1.1270    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  3  1  1  0  0  0  0
  4  2  1  0  0  0  0
  5  3  1  0  0  0  0
  5  4  1  0  0  0  0
  6  1  1  0  0  0  0
  7  3  2  0  0  0  0
  4  8  1  1  0  0  0
  5  9  1  6  0  0  0
 13  2  1  0  0  0  0
 14 10  1  0  0  0  0
 14 11  1  0  0  0  0
 14 12  2  0  0  0  0
 14 13  1  0  0  0  0
  4 15  1  1  0  0  0
  5 16  1  6  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030075

> <DATABASE_NAME>
MIME

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

> <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)/t4-,5+/m0/s1

> <INCHI_KEY>
FNZLKVNUWIIPSJ-CRCLSJGQSA-N

> <FORMULA>
C5H11O8P

> <MOLECULAR_WEIGHT>
230.1098

> <EXACT_MASS>
230.01915384

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
18.04912458941236

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.81

> <JCHEM_LOGP>
-2.7602629813333333

> <ALOGPS_LOGS>
-0.95

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.504370847667954

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.4785529591465414

> <JCHEM_PKA_STRONGEST_BASIC>
-3.3276267100529333

> <JCHEM_POLAR_SURFACE_AREA>
144.52

> <JCHEM_REFRACTIVITY>
42.4722

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.61e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
L-ribulose 5-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 13-AUG-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   13-AUG-12         0                                  
HETATM    1  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.000   0.000   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   15  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3    6                                                       
CONECT    2    4   13                                                       
CONECT    3    1    5    7                                                  
CONECT    4    2    5    8   15                                             
CONECT    5    3    4    9   16                                             
CONECT    6    1                                                            
CONECT    7    3                                                            
CONECT    8    4                                                            
CONECT    9    5                                                            
CONECT   10   14                                                            
CONECT   11   14                                                            
CONECT   12   14                                                            
CONECT   13    2   14                                                       
CONECT   14   10   11   12   13                                             
CONECT   15    4                                                            
CONECT   16    5                                                            
MASTER        0    0    0    0    0    0    0    0   16    0   30    0
END

Synonyms

Value	Source
5-O-Phosphono-L-erythro-pent-2-ulose	ChEBI
5-O-Phosphono-L-ribulose	ChEBI
L-Ribulose 5-phosphoric acid	Generator
Ribulose 5-phosphate	MeSH
Ribulose 5-phosphate, (D)-isomer	MeSH
Ribulose 5-phosphate, (L)-isomer	MeSH

Molecular Formula

C₅H₁₁O₈P

Average Mass

230.1098

Monoisotopic Mass

230.01915384

IUPAC Name

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

Traditional Name

L-ribulose 5-phosphate

CAS Registry Number

2922-69-2

SMILES

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

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)/t4-,5+/m0/s1

InChI Key

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

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

ribulose 5-phosphate (CHEBI:17666 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	26.1 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.8	ChemAxon
logS	-0.95	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	5	ChemAxon
Polar Surface Area	144.52 Å²	ChemAxon
Rotatable Bond Count	6	ChemAxon
Refractivity	42.47 m³·mol⁻¹	ChemAxon
Polarizability	18.05 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

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01q9-3790000000-2c11b3331f617fcac827	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0btd-9710000000-28813a9eaf50967c87e7	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0a4i-9200000000-5ba5e3b7a9495a17a555	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002r-9520000000-88185c13004c51d8fbb9	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-4b58e89007a1a7f893dd	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-8cddc9cbb874799a0ced	2015-09-15	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-21	View Spectrum

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

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
MMDBr0007139	Adenosine triphosphate	ADP	Not Available	L-ribulokinase (L-ribulose)	VMH	30371894
MMDBr0007140	L-Ribulose 5-phosphate	Xylulose 5-phosphate	Not Available	L-ribulose-phosphate 4-epimerase	VMH	30371894
MMDBr0007954	L-Ribulose 5-phosphate	L-Xylulose 5-phosphate	Not Available	L-ribulose-5-phosphate 3-epimerase	VMH	30371894
MMDBr0013774	L-Ribulose 5-phosphate	L-Xylulose 5-phosphate	Putative L-ribulose-5-phosphate 3-epimerase SgbU	Epimerization	RHEA	34755880
MMDBr0014169	Adenosine triphosphate	ADP	Ribulokinase	Phosphorylation	RHEA	34755880
MMDBr0014198	L-Ribulose 5-phosphate	Xylulose 5-phosphate	L-ribulose-5-phosphate 4-epimerase	Epimerization	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	Proteobacteria	213	Human feces; Human ; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human sputum; Human unknown	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	368	Human feces; Human pleural fluid plaque; Human ; Human subgingival plaque; Human saliva; Human stool; Cattle ; Pig	Metabolic reconstruction
Bacteria	Actinobacteria	111	Human feces; Human ; Human supragingival plaque; Human mucosa; Human saliva; Human subgingival plaque; Human pleural fluid plaque; Human dental plaque; Human sputum; Human nasopharyngeal swab	Metabolic reconstruction
Bacteria	Bacteroidetes	114	Human feces; Human appendix biopsy; Human stool; Human saliva; Human ; Human gastric fluid; Human urine; Human supragingival plaque; Human subgingival plaque	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Bacteria	Tenericutes	5	Human feces; Human	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Synergistetes	2	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	19	Human feces; Human	Metabolic reconstruction

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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

Not Available

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

C00019543

Chemspider ID

Not Available

KEGG Compound ID

C01101

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

439399

PDB ID

Not Available

ChEBI ID

17666

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]
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 L-Ribulose 5-phosphate (MMDBc0030075)

MOL for #<Metabolite:0x00007fe27d48ba18>

3D MOL for #<Metabolite:0x00007fe27d48ba18>

3D SDF for #<Metabolite:0x00007fe27d48ba18>

3D-SDF for #<Metabolite:0x00007fe27d48ba18>

PDB for #<Metabolite:0x00007fe27d48ba18>

3D PDB for #<Metabolite:0x00007fe27d48ba18>

SMILES for #<Metabolite:0x00007fe27d48ba18>

INCHI for #<Metabolite:0x00007fe27d48ba18>

Structure for #<Metabolite:0x00007fe27d48ba18>

3D Structure for #<Metabolite:0x00007fe27d48ba18>