MiMeDB: Showing metabocard for D-xylulose 1,5-bisphosphate (MMDBc0054444)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 23:12:37 UTC

Update Date

2022-08-12 20:09:00 UTC

Metabolite ID

MMDBc0054444

Metabolite Identification

Common Name

D-xylulose 1,5-bisphosphate

Description

D-xylulose 1,5-bisphosphate, also known as D-threo-2-pentulose, 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. D-xylulose 1,5-bisphosphate is an extremely weak basic (essentially neutral) compound (based on its pKa).

Structure

MOL SDF PDB SMILES InChI


  Mrv0541 05041413172D          

 20 19  0  0  1  0            999 V2000
    3.7125   -2.1434    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2375   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.3000   -1.4289    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.0625   -0.7145    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -1.4289    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    3.7125   -0.7145    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.4750   -0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0625   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.3625   -3.5724    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6645   -2.4454    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2355   -3.2704    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000   -0.8250    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.5375   -2.1434    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.8250    0.0000    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.9500   -2.8579    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    0.0000    0.0000    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -2.1434    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8875   -0.7145    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
  3  6  1  1  0  0  0
  7  4  2  0  0  0  0
  5  8  1  1  0  0  0
 15  1  1  0  0  0  0
 16  2  1  0  0  0  0
 17  9  1  0  0  0  0
 17 10  1  0  0  0  0
 17 11  2  0  0  0  0
 17 15  1  0  0  0  0
 18 12  1  0  0  0  0
 18 13  1  0  0  0  0
 18 14  2  0  0  0  0
 18 16  1  0  0  0  0
  3 19  1  1  0  0  0
  5 20  1  1  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054444

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3,5-6,8H,1-2H2,(H2,9,10,11)(H2,12,13,14)/t3-,5+/m1/s1

> <INCHI_KEY>
YAHZABJORDUQGO-WUJLRWPWSA-N

> <FORMULA>
C5H12O11P2

> <MOLECULAR_WEIGHT>
310.0897

> <EXACT_MASS>
309.98548425

> <JCHEM_ACCEPTOR_COUNT>
9

> <JCHEM_AVERAGE_POLARIZABILITY>
22.650072420140706

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
6

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.49

> <JCHEM_LOGP>
-2.8838290126666664

> <ALOGPS_LOGS>
-1.41

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-4

> <JCHEM_PKA>
1.6549995885319904

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.0021606343762866

> <JCHEM_PKA_STRONGEST_BASIC>
-3.5803636984429508

> <JCHEM_POLAR_SURFACE_AREA>
191.04999999999995

> <JCHEM_REFRACTIVITY>
53.345099999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
8

> <JCHEM_RULE_OF_FIVE>
0

> <ALOGPS_SOLUBILITY>
1.21e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
[(3S,4R)-3,4-dihydroxy-2-oxo-5-(phosphonooxy)pentyl]oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 04-MAY-14   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   04-MAY-14         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  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   15  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   16  O   UNK     0       0.000   0.000   0.000  0.00  0.00           O+0
HETATM   17  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   18  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   19  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
HETATM   20  H   UNK     0       0.000   0.000   0.000  0.00  0.00           H+0
CONECT    1    3   15                                                       
CONECT    2    4   16                                                       
CONECT    3    1    5    6   19                                             
CONECT    4    2    5    7                                                  
CONECT    5    3    4    8   20                                             
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9   17                                                            
CONECT   10   17                                                            
CONECT   11   17                                                            
CONECT   12   18                                                            
CONECT   13   18                                                            
CONECT   14   18                                                            
CONECT   15    1   17                                                       
CONECT   16    2   18                                                       
CONECT   17    9   10   11   15                                             
CONECT   18   12   13   14   16                                             
CONECT   19    3                                                            
CONECT   20    5                                                            
MASTER        0    0    0    0    0    0    0    0   20    0   38    0
END

Synonyms

Value	Source
D-Threo-2-pentulose	ChEBI
D-Xylulose 1,5-bis(dihydrogen phosphate)	ChEBI
Xylulose 1,5-bisphosphate	ChEBI
D-Xylulose 1,5-bis(dihydrogen phosphoric acid)	Generator
Xylulose 1,5-bisphosphoric acid	Generator
D-Xylulose 1,5-bisphosphoric acid	Generator
Xylulose 1,5-diphosphate	MeSH

Molecular Formula

C₅H₁₂O₁₁P₂

Average Mass

310.0897

Monoisotopic Mass

309.98548425

IUPAC Name

{[(3S,4R)-3,4-dihydroxy-2-oxo-5-(phosphonooxy)pentyl]oxy}phosphonic acid

Traditional Name

[(3S,4R)-3,4-dihydroxy-2-oxo-5-(phosphonooxy)pentyl]oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H12O11P2/c6-3(1-15-17(9,10)11)5(8)4(7)2-16-18(12,13)14/h3,5-6,8H,1-2H2,(H2,9,10,11)(H2,12,13,14)/t3-,5+/m1/s1

InChI Key

YAHZABJORDUQGO-WUJLRWPWSA-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-5-phosphate
Pentose phosphate
Glycerone phosphate
Monosaccharide phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Beta-hydroxy ketone
Acyloin
Alpha-hydroxy ketone
Secondary alcohol
Ketone
1,2-diol
Organic oxide
Hydrocarbon derivative
Carbonyl group
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

Not Available

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	12.1 g/L	ALOGPS
logP	-1.5	ALOGPS
logP	-2.9	ChemAxon
logS	-1.4	ALOGPS
pKa (Strongest Acidic)	1	ChemAxon
pKa (Strongest Basic)	-3.6	ChemAxon
Physiological Charge	-4	ChemAxon
Hydrogen Acceptor Count	9	ChemAxon
Hydrogen Donor Count	6	ChemAxon
Polar Surface Area	191.05 Å²	ChemAxon
Rotatable Bond Count	8	ChemAxon
Refractivity	53.35 m³·mol⁻¹	ChemAxon
Polarizability	22.65 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

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

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

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

167298

PDB ID

Not Available

ChEBI ID

138937

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-xylulose 1,5-bisphosphate (MMDBc0054444)

MOL for #<Metabolite:0x00007f9238d71078>

3D MOL for #<Metabolite:0x00007f9238d71078>

3D SDF for #<Metabolite:0x00007f9238d71078>

3D-SDF for #<Metabolite:0x00007f9238d71078>

PDB for #<Metabolite:0x00007f9238d71078>

3D PDB for #<Metabolite:0x00007f9238d71078>

SMILES for #<Metabolite:0x00007f9238d71078>

INCHI for #<Metabolite:0x00007f9238d71078>

Structure for #<Metabolite:0x00007f9238d71078>

3D Structure for #<Metabolite:0x00007f9238d71078>