MiMeDB: Showing metabocard for D-Ribulose-1-phosphate (MMDBc0030182)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:57:21 UTC

Update Date

2024-04-30 19:44:46 UTC

Metabolite ID

MMDBc0030182

Metabolite Identification

Common Name

D-Ribulose-1-phosphate

Description

D-ribulose-1-phosphate is a pentose phosphate. Pentoses are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Structure

MOL 3D MOL SDF 3D SDF PDB 3D PDB SMILES InChI

Structure #1
  Mrv0541 02241207302D          

 14 13  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  0  0  0  0  0  0  0  0  0  0
    0.3020   -0.3020    0.0000 C   0  0  0  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  3  1  0  0  0  0
  1  6  1  0  0  0  0
  2  4  1  0  0  0  0
  2 13  1  0  0  0  0
  3  5  1  0  0  0  0
  3  7  1  0  0  0  0
  4  5  1  0  0  0  0
  4  8  2  0  0  0  0
  5  9  1  0  0  0  0
 10 14  1  0  0  0  0
 11 14  1  0  0  0  0
 12 14  2  0  0  0  0
 13 14  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0030182

> <DATABASE_NAME>
MIME

> <SMILES>
OCC(O)C(O)C(=O)COP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3,5-7,9H,1-2H2,(H2,10,11,12)

> <INCHI_KEY>
NBOCCPQHBPGYCX-UHFFFAOYSA-N

> <FORMULA>
C5H11O8P

> <MOLECULAR_WEIGHT>
230.1098

> <EXACT_MASS>
230.01915384

> <JCHEM_ACCEPTOR_COUNT>
7

> <JCHEM_AVERAGE_POLARIZABILITY>
18.070378526223664

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
5

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

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

> <ALOGPS_LOGP>
-1.80

> <JCHEM_LOGP>
-2.7602629813333333

> <ALOGPS_LOGS>
-0.97

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.208722028772268

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.1786190642675627

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9797461037901494

> <JCHEM_POLAR_SURFACE_AREA>
144.52

> <JCHEM_REFRACTIVITY>
42.4722

> <JCHEM_ROTATABLE_BOND_COUNT>
6

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
2.47e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
(3,4,5-trihydroxy-2-oxopentyl)oxyphosphonic acid

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 24-FEB-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: Structure #1                                      
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   24-FEB-12         0                                  
HETATM    1  C   UNK     0      -2.104  -0.564   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       3.231  -0.564   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      -0.770  -1.334   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       1.897  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.564  -0.564   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      -3.437  -1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -0.770  -2.874   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       1.897  -2.874   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0       0.564   0.976   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       7.232   0.206   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       6.668  -1.897   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       5.128   0.770   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0       4.565  -1.334   0.000  0.00  0.00           O+0
HETATM   14  P   UNK     0       5.898  -0.564   0.000  0.00  0.00           P+0
CONECT    1    3    6                                                       
CONECT    2    4   13                                                       
CONECT    3    1    5    7                                                  
CONECT    4    2    5    8                                                  
CONECT    5    3    4    9                                                  
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                                             
MASTER        0    0    0    0    0    0    0    0   14    0   26    0
END

Synonyms

Value	Source
D-Ribulose-1-phosphoric acid	Generator

Molecular Formula

C₅H₁₁O₈P

Average Mass

230.1098

Monoisotopic Mass

230.01915384

IUPAC Name

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

Traditional Name

(3,4,5-trihydroxy-2-oxopentyl)oxyphosphonic acid

CAS Registry Number

Not Available

SMILES

OCC(O)C(O)C(=O)COP(O)(O)=O

InChI Identifier

InChI=1S/C5H11O8P/c6-1-3(7)5(9)4(8)2-13-14(10,11)12/h3,5-7,9H,1-2H2,(H2,10,11,12)

InChI Key

NBOCCPQHBPGYCX-UHFFFAOYSA-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

Monosaccharide phosphate
Pentose monosaccharide
Glycerone phosphate
Monoalkyl 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
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	24.7 g/L	ALOGPS
logP	-1.8	ALOGPS
logP	-2.8	ChemAxon
logS	-0.97	ALOGPS
pKa (Strongest Acidic)	1.18	ChemAxon
pKa (Strongest Basic)	-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	18.07 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 (Non-derivatized) - 70eV, Positive	splash10-03dr-9400000000-7269865221c503b136dd	2021-09-24	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_1_6) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_3) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_4) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_5) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_6) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_7) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_8) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_9) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_10) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_11) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_12) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_13) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_14) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_2_15) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_1) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (TMS_3_2) - 70eV, Positive	Not Available	2021-11-05	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-01q9-6790000000-b78930667ee220f97c87	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-03dr-7910000000-c95b21fe4d80a23880ae	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0btd-9200000000-e990a2097079623f75eb	2015-09-14	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-00p0-9520000000-cceac28c0a4d803814b1	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-bc52e0e96b120d80bffd	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-4bba371361aef9717f61	2015-09-15	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-10-27	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-10-27	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
MMDBr0019221	D-Ribulose	Hydrogen Ion	L-fuculokinase	Phosphorylation	PathBank	31602464
MMDBr0019222	D-Ribulose-1-phosphate	Glycolaldehyde	L-fuculose phosphate aldolase	Aldol addition (or reverse)	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	Proteobacteria	1	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool	Unknown

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

HMDB0260227

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

Not Available

KNApSAcK ID

Not Available

Chemspider ID

595

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

615

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Barupal DK, Fiehn O: Generating the Blood Exposome Database Using a Comprehensive Text Mining and Database Fusion Approach. Environ Health Perspect. 2019 Sep;127(9):97008. doi: 10.1289/EHP4713. Epub 2019 Sep 26. [PubMed:31557052 ]

Showing metabocard for D-Ribulose-1-phosphate (MMDBc0030182)

MOL for #<Metabolite:0x00007fa5089da4b8>

3D MOL for #<Metabolite:0x00007fa5089da4b8>

3D SDF for #<Metabolite:0x00007fa5089da4b8>

3D-SDF for #<Metabolite:0x00007fa5089da4b8>

PDB for #<Metabolite:0x00007fa5089da4b8>

3D PDB for #<Metabolite:0x00007fa5089da4b8>

SMILES for #<Metabolite:0x00007fa5089da4b8>

INCHI for #<Metabolite:0x00007fa5089da4b8>

Structure for #<Metabolite:0x00007fa5089da4b8>

3D Structure for #<Metabolite:0x00007fa5089da4b8>