MiMeDB: Showing metabocard for 5-deoxy-D-ribulose 1-phosphate (MMDBc0055558)

Record Information

Version

2.0

Status

Detected and Quantified

Creation Date

2022-06-17 19:58:50 UTC

Update Date

2025-10-07 16:09:12 UTC

Metabolite ID

MMDBc0055558

Metabolite Identification

Common Name

5-deoxy-D-ribulose 1-phosphate

Description

5-deoxy-D-ribulose 1-phosphate is a carbohydrate metabolite belonging to the class of phosphorylated sugars. There is limited literature available on this metabolite, indicating a need for further research to understand its biological significance and potential roles in metabolic pathways.

Structure

MOL SDF PDB SMILES InChI


  Mrv1652306172221582D          

 15 14  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  2  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
   -0.8250    0.0000    0.0000 O   0  5  0  0  0  0  0  0  0  0  0  0
    0.0000    0.8250    0.0000 O   0  5  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
    0.8250    0.0000    0.0000 O   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  6  0  0  0
 12  2  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  1  0  0  0  0
 13 11  2  0  0  0  0
 13 12  1  0  0  0  0
  3 14  1  1  0  0  0
  5 15  1  6  0  0  0
M  CHG  2   9  -1  10  -1
M  END
> <DATABASE_ID>
MMDBc0055558

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h3,5-6,8H,2H2,1H3,(H2,9,10,11)/p-2/t3-,5-/m1/s1

> <INCHI_KEY>
AVEHMJVDRGMBHD-NQXXGFSBSA-L

> <FORMULA>
C5H9O7P

> <MOLECULAR_WEIGHT>
212.095

> <EXACT_MASS>
212.009686788

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_ATOM_COUNT>
22

> <JCHEM_AVERAGE_POLARIZABILITY>
16.692884838913564

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
2

> <JCHEM_FORMAL_CHARGE>
-2

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(3R,4R)-3,4-dihydroxy-1-(phosphonooxy)pentan-2-one

> <JCHEM_LOGP>
-1.7133530146666665

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.208915403004367

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.17880946300793

> <JCHEM_PKA_STRONGEST_BASIC>
-3.088183511814785

> <JCHEM_POLAR_SURFACE_AREA>
129.95000000000002

> <JCHEM_REFRACTIVITY>
38.685100000000006

> <JCHEM_ROTATABLE_BOND_COUNT>
5

> <JCHEM_RULE_OF_FIVE>
1

> <JCHEM_TRADITIONAL_IUPAC>
(3R,4R)-3,4-dihydroxy-1-(phosphonooxy)pentan-2-one

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUN-22   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUN-22         0                                  
HETATM    1  C   UNK     0       6.930  -4.001   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.310  -1.334   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       6.160  -2.667   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0       3.850  -1.334   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       4.620  -2.667   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       6.930  -1.334   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0       4.620  -0.000   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       3.850  -4.001   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.540   0.000   0.000  0.00  0.00           O-1
HETATM   10  O   UNK     0       0.000   1.540   0.000  0.00  0.00           O-1
HETATM   11  O   UNK     0       0.000  -1.540   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       1.540   0.000   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0       0.000   0.000   0.000  0.00  0.00           P+0
HETATM   14  H   UNK     0       5.390  -4.001   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       5.390  -1.334   0.000  0.00  0.00           H+0
CONECT    1    3                                                            
CONECT    2    4   12                                                       
CONECT    3    1    5    6   14                                             
CONECT    4    2    5    7                                                  
CONECT    5    3    4    8   15                                             
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8    5                                                            
CONECT    9   13                                                            
CONECT   10   13                                                            
CONECT   11   13                                                            
CONECT   12    2   13                                                       
CONECT   13    9   10   11   12                                             
CONECT   14    3                                                            
CONECT   15    5                                                            
MASTER        0    0    0    0    0    0    0    0   15    0   28    0
END

Synonyms

Value	Source
5-Deoxy-D-ribulose 1-phosphoric acid	Generator

Molecular Formula

C₅H₉O₇P

Average Mass

212.095

Monoisotopic Mass

212.009686788

IUPAC Name

(3R,4R)-3,4-dihydroxy-1-(phosphonooxy)pentan-2-one

Traditional Name

(3R,4R)-3,4-dihydroxy-1-(phosphonooxy)pentan-2-one

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H11O7P/c1-3(6)5(8)4(7)2-12-13(9,10)11/h3,5-6,8H,2H2,1H3,(H2,9,10,11)/p-2/t3-,5-/m1/s1

InChI Key

AVEHMJVDRGMBHD-NQXXGFSBSA-L

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as glycerone phosphates. These are organic compounds containing a glycerone moiety that carries a phosphate group at the O-1 or O-2 position.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbonyl compounds

Direct Parent

Glycerone phosphates

Alternative Parents

Substituents

Glycerone phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Monosaccharide
Beta-hydroxy ketone
Acyloin
Alpha-hydroxy ketone
Secondary alcohol
1,2-diol
Organic oxide
Hydrocarbon derivative
Alcohol
Organic anion
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
logP	-1.7	ChemAxon
pKa (Strongest Acidic)	1.18	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	2	ChemAxon
Polar Surface Area	129.95 Å²	ChemAxon
Rotatable Bond Count	5	ChemAxon
Refractivity	38.69 m³·mol⁻¹	ChemAxon
Polarizability	16.69 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	Deposition Date	View
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

Chromatographic Retention Times and Retention Indices

Retention Times

Chromatography Type	Technique	Column	Deposition Date	Retention Time (s)
Liquid Chromatography	HILIC	Waters Acquity UPLC-BEH Amide column (eluted)	2025-10-24	320.6
Liquid Chromatography	HILIC	Accucore 150 Amide HILIC (eluted)	2025-10-24	165.6
Liquid Chromatography	Reversed-phase	Hypersil Gold 1.9 µm C18 (eluted)	2025-10-24	133.1
Liquid Chromatography	Reversed-phase	Agilent Zorbax Eclipse Plus C18 (2.1 mm x 150 mm, 3.5 um) (eluted)	2025-10-24	352.9
Liquid Chromatography	Reversed-phase	XBridge C18 3.5u 2.1x50 mm (eluted)	2025-10-24	264.6
Liquid Chromatography	Reversed-phase	Ascentis Express C18 (void)	2025-10-24	311.3
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (void)	2025-10-24	1032.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	138.7
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC (eluted)	2025-10-24	821.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	179.3
Liquid Chromatography	HILIC	Merck SeQuant ZIC-HILIC (eluted)	2025-10-24	211.6
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC HSS T3 C18 (eluted)	2025-10-24	170.9
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (eluted)	2025-10-24	57.5
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	354.8
Liquid Chromatography	HILIC	Merck SeQuant ZIC-pHILIC column (eluted)	2025-10-24	576.8
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	50.7
Liquid Chromatography	Reversed-phase	Waters ACQUITY UPLC BEH C18 (void)	2025-10-24	218.1
Liquid Chromatography	Reversed-phase	Kinetex Core-Shell C18 2.6 um, 3.0 x 100 mm, Phenomenex (eluted)	2025-10-24	900.4
Liquid Chromatography	Reversed-phase	Waters Atlantis T3 (2.1 x 150 mm, 5 um) (eluted)	2025-10-24	625.1

Retention Indices

Chromatography Type	Peak Label	SMILES	Stationary Phase	Deposition Date	Retention Index
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_1	C[C@@H](O[Si](C)(C)C)[C@@H](O)C(=O)COP(=O)([O-])[O-]	standard non polar	2025-10-24	1514.63
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_2	C[C@@H](O)[C@@H](O[Si](C)(C)C)C(=O)COP(=O)([O-])[O-]	standard non polar	2025-10-24	1686.08
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_3	C[C@@H](O)C(O)=C(COP(=O)([O-])[O-])O[Si](C)(C)C	standard non polar	2025-10-24	1462.44
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_4	C[C@@H](O)[C@@H](O)C(=COP(=O)([O-])[O-])O[Si](C)(C)C	standard non polar	2025-10-24	1904.91
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_5	C[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)COP(=O)([O-])[O-]	standard non polar	2025-10-24	2125.61
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_6	C[C@@H](O[Si](C)(C)C)C(O)=C(COP(=O)([O-])[O-])O[Si](C)(C)C	standard non polar	2025-10-24	2097.93
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_7	C[C@@H](O[Si](C)(C)C)[C@@H](O)C(=COP(=O)([O-])[O-])O[Si](C)(C)C	standard non polar	2025-10-24	2333.14
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_8	C[C@@H](O)C(O[Si](C)(C)C)=C(COP(=O)([O-])[O-])O[Si](C)(C)C	standard non polar	2025-10-24	1722.05
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_9	C[C@@H](O)[C@@H](O[Si](C)(C)C)C(=COP(=O)([O-])[O-])O[Si](C)(C)C	standard non polar	2025-10-24	1555.39
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_10	C[C@@H](O[Si](C)(C)C)C(O[Si](C)(C)C)=C(COP(=O)([O-])[O-])O[Si](C)(C)C	standard non polar	2025-10-24	2294.55
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_11	C[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=COP(=O)([O-])[O-])O[Si](C)(C)C	standard non polar	2025-10-24	1575.8
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_1	C[C@@H](O[Si](C)(C)C)[C@@H](O)C(=O)COP(=O)([O-])[O-]	standard polar	2025-10-24	2023.91
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_2	C[C@@H](O)[C@@H](O[Si](C)(C)C)C(=O)COP(=O)([O-])[O-]	standard polar	2025-10-24	2124.01
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_3	C[C@@H](O)C(O)=C(COP(=O)([O-])[O-])O[Si](C)(C)C	standard polar	2025-10-24	1914.57
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_4	C[C@@H](O)[C@@H](O)C(=COP(=O)([O-])[O-])O[Si](C)(C)C	standard polar	2025-10-24	2749.13
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_5	C[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=O)COP(=O)([O-])[O-]	standard polar	2025-10-24	2582.07
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_6	C[C@@H](O[Si](C)(C)C)C(O)=C(COP(=O)([O-])[O-])O[Si](C)(C)C	standard polar	2025-10-24	1973.1
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_7	C[C@@H](O[Si](C)(C)C)[C@@H](O)C(=COP(=O)([O-])[O-])O[Si](C)(C)C	standard polar	2025-10-24	2156.28
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_8	C[C@@H](O)C(O[Si](C)(C)C)=C(COP(=O)([O-])[O-])O[Si](C)(C)C	standard polar	2025-10-24	2348.21
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_9	C[C@@H](O)[C@@H](O[Si](C)(C)C)C(=COP(=O)([O-])[O-])O[Si](C)(C)C	standard polar	2025-10-24	1804.47
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_10	C[C@@H](O[Si](C)(C)C)C(O[Si](C)(C)C)=C(COP(=O)([O-])[O-])O[Si](C)(C)C	standard polar	2025-10-24	1408.79
Gas Chromatography	5-deoxy-D-ribulose 1-phosphate_TMS_11	C[C@@H](O[Si](C)(C)C)[C@@H](O[Si](C)(C)C)C(=COP(=O)([O-])[O-])O[Si](C)(C)C	standard polar	2025-10-24	1634.08

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

Microbial Pathways

Pathways

Not Available

Metabolic Reactions

Reactions

This table shows at most 20 reactions. For the full list of associated reactions:

See All Associated 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
Bacteria/Eubacteria	Firmicutes	15	Human ; Human feces
Bacteria	Firmicutes	1	Human ; Human feces
Bacteria/Eubacteria	Thermotogae	1
Bacteria/Eubacteria	Proteobacteria	2	Human

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

77422009

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

134930915

PDB ID

Not Available

ChEBI ID

Not Available

Food Biomarker Ontology

Not Available

CMMC Knowledgebase

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 5-deoxy-D-ribulose 1-phosphate (MMDBc0055558)

MOL for #<Metabolite:0x00007f9acfe02420>

3D MOL for #<Metabolite:0x00007f9acfe02420>

3D SDF for #<Metabolite:0x00007f9acfe02420>

3D-SDF for #<Metabolite:0x00007f9acfe02420>

PDB for #<Metabolite:0x00007f9acfe02420>

3D PDB for #<Metabolite:0x00007f9acfe02420>

SMILES for #<Metabolite:0x00007f9acfe02420>

INCHI for #<Metabolite:0x00007f9acfe02420>

Structure for #<Metabolite:0x00007f9acfe02420>

3D Structure for #<Metabolite:0x00007f9acfe02420>