MiMeDB: Showing metabocard for 2-deoxy-alpha-D-ribose 1-phosphate (MMDBc0054164)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-06-05 22:56:42 UTC

Update Date

2022-09-01 02:27:38 UTC

Metabolite ID

MMDBc0054164

Metabolite Identification

Common Name

2-deoxy-alpha-D-ribose 1-phosphate

Description

Structure

MOL SDF PDB SMILES InChI

 
  Mrv0541 07171214072D          
 
 13 13  0  0  1  0            999 V2000
   15.9078  -12.3959    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   15.2380  -11.9193    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   15.6542  -13.1868    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   16.6910  -12.1387    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   14.5758  -12.3959    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   14.8255  -13.1868    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   17.5121  -12.1387    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   13.7963  -12.1387    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   14.3412  -13.8491    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   18.3332  -12.1387    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5084  -11.3137    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   17.5084  -12.9598    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   13.6260  -11.3327    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  1  2  1  0  0  0  0
  1  3  1  0  0  0  0
  1  4  1  6  0  0  0
  2  5  1  0  0  0  0
  3  6  1  0  0  0  0
  4  7  1  0  0  0  0
  5  8  1  1  0  0  0
  6  9  1  6  0  0  0
  7 10  1  0  0  0  0
  7 11  1  0  0  0  0
  7 12  2  0  0  0  0
  8 13  1  0  0  0  0
  5  6  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0054164

> <DATABASE_NAME>
MIME

> <SMILES>
OC[C@H]1O[C@@H](C[C@@H]1O)OP(O)(O)=O

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O7P/c6-2-4-3(7)1-5(11-4)12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1

> <INCHI_KEY>
KBDKAJNTYKVSEK-VPENINKCSA-N

> <FORMULA>
C5H11O7P

> <MOLECULAR_WEIGHT>
214.1104

> <EXACT_MASS>
214.024239218

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
17.344215869263515

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-2.14

> <JCHEM_LOGP>
-1.5251322443333333

> <ALOGPS_LOGS>
-0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.425838614205934

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.3651983750806824

> <JCHEM_PKA_STRONGEST_BASIC>
-2.9789480049262043

> <JCHEM_POLAR_SURFACE_AREA>
116.45

> <JCHEM_REFRACTIVITY>
39.3231

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.76e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
2-deoxy-α-D-ribose 1-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 17-JUL-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE:                                                   
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   17-JUL-12         0                                  
HETATM    1  C   UNK     0      29.695 -23.139   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      28.444 -22.249   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      29.221 -24.615   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0      31.156 -22.659   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      27.208 -23.139   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      27.674 -24.615   0.000  0.00  0.00           C+0
HETATM    7  P   UNK     0      32.689 -22.659   0.000  0.00  0.00           P+0
HETATM    8  C   UNK     0      25.753 -22.659   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      26.770 -25.852   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      34.222 -22.659   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      32.682 -21.119   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      32.682 -24.192   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      25.435 -21.154   0.000  0.00  0.00           O+0
CONECT    1    2    3    4                                                  
CONECT    2    1    5                                                       
CONECT    3    1    6                                                       
CONECT    4    1    7                                                       
CONECT    5    2    8    6                                                  
CONECT    6    3    9    5                                                  
CONECT    7    4   10   11   12                                             
CONECT    8    5   13                                                       
CONECT    9    6                                                            
CONECT   10    7                                                            
CONECT   11    7                                                            
CONECT   12    7                                                            
CONECT   13    8                                                            
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

Synonyms

Value	Source
2-Deoxy-1-O-phosphono-alpha-D-erythro-pentofuranose	ChEBI
2-Deoxy-1-O-phosphono-a-D-erythro-pentofuranose	Generator
2-Deoxy-1-O-phosphono-α-D-erythro-pentofuranose	Generator
2-Deoxy-a-D-ribose 1-phosphate	Generator
2-Deoxy-a-D-ribose 1-phosphoric acid	Generator
2-Deoxy-alpha-D-ribose 1-phosphoric acid	Generator
2-Deoxy-α-D-ribose 1-phosphate	Generator
2-Deoxy-α-D-ribose 1-phosphoric acid	Generator
2-Deoxyribose 1-phosphate, (beta-D-erythro)-isomer	MeSH
2-Deoxyribose 1-phosphate	MeSH
2-Deoxyribose 1-phosphate, (alpha-D-erythro)-isomer	MeSH
2-Deoxy-alpha-D-ribose 1-phosphate	KEGG
2-Deoxy-D-ribose 1-phosphoric acid	Generator

Molecular Formula

C₅H₁₁O₇P

Average Mass

214.1104

Monoisotopic Mass

214.024239218

IUPAC Name

{[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}phosphonic acid

Traditional Name

2-deoxy-α-D-ribose 1-phosphate

CAS Registry Number

Not Available

SMILES

OC[C@H]1O[C@@H](C[C@@H]1O)OP(O)(O)=O

InChI Identifier

InChI=1S/C5H11O7P/c6-2-4-3(7)1-5(11-4)12-13(8,9)10/h3-7H,1-2H2,(H2,8,9,10)/t3-,4+,5+/m0/s1

InChI Key

KBDKAJNTYKVSEK-VPENINKCSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Pentoses

Alternative Parents

Substituents

Pentose monosaccharide
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Tetrahydrofuran
Secondary alcohol
Oxacycle
Organoheterocyclic compound
Organic oxide
Hydrocarbon derivative
Primary alcohol
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

2-deoxy-D-ribofuranose 1-phosphate (CHEBI:11563 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	37.6 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-1.5	ChemAxon
logS	-0.76	ALOGPS
pKa (Strongest Acidic)	1.37	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-2	ChemAxon
Hydrogen Acceptor Count	6	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	116.45 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	39.32 m³·mol⁻¹	ChemAxon
Polarizability	17.34 Å³	ChemAxon
Number of Rings	1	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_1) - 70eV, Positive	Not Available	2022-08-08	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-9330000000-6562929eed9357e7e9d1	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9400000000-274b8482009b447be080	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-9200000000-8f81db5c1c525c0b2928	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03fs-9170000000-3bd4c0ef1636dae0eb80	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-fad5f64e9702b6afeb86	2019-02-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-6c7bb204da84c6b447f2	2019-02-23	View Spectrum
MS	Mass Spectrum (Electron Ionization)	Not Available	2022-08-06	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
MMDBr0013488	Phosphate	2-deoxy-alpha-D-ribose 1-phosphate	Pyrimidine-nucleoside phosphorylase	Phosphorylation	RHEA	34755880
MMDBr0014255	2'-Deoxyuridine	2-deoxy-alpha-D-ribose 1-phosphate	Pyrimidine-nucleoside phosphorylase	Phosphorylation	RHEA	34755880
MMDBr0014728	Deoxyguanosine	2-deoxy-alpha-D-ribose 1-phosphate	Purine nucleoside phosphorylase DeoD-type	Phosphorylation	RHEA	34755880
MMDBr0014729	Deoxyinosine	2-deoxy-alpha-D-ribose 1-phosphate	Purine nucleoside phosphorylase DeoD-type	Phosphorylation	RHEA	34755880
MMDBr0024826	2-deoxy-alpha-D-ribose 1-phosphate	Deoxyribose 5-phosphate	Phosphopentomutase	Transfers of a phosphate group; Isomerization; Intramolecular transfer of functional group	RHEA	34755880
MMDBr0024827	Deoxyadenosine	Adenine	Purine nucleoside phosphorylase DeoD-type	Phosphorylation	RHEA	34755880
MMDBr0024957	Phosphate	2-deoxy-alpha-D-ribose 1-phosphate	Purine nucleoside phosphorylase	Phosphorylation	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
Bacteria	Firmicutes	17	Human feces; Human ; Cattle
Bacteria	Proteobacteria	214	Human ; Human feces; River trout ; Cattle
Bacteria	Chlorobi	1
Bacteria	Spirochaetes	4	Human
Bacteria	Actinobacteria	3	Human
Bacteria	Planctomycetes	1
Bacteria/NULL	Proteobacteria	1	Human ; Human feces; River trout ; Cattle
Bacteria	Tenericutes	4	Human

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

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

C00672

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

5460448

PDB ID

Not Available

ChEBI ID

11563

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 2-deoxy-alpha-D-ribose 1-phosphate (MMDBc0054164)

MOL for #<Metabolite:0x00007f5a90527a00>

3D MOL for #<Metabolite:0x00007f5a90527a00>

3D SDF for #<Metabolite:0x00007f5a90527a00>

3D-SDF for #<Metabolite:0x00007f5a90527a00>

PDB for #<Metabolite:0x00007f5a90527a00>

3D PDB for #<Metabolite:0x00007f5a90527a00>

SMILES for #<Metabolite:0x00007f5a90527a00>

INCHI for #<Metabolite:0x00007f5a90527a00>

Structure for #<Metabolite:0x00007f5a90527a00>

3D Structure for #<Metabolite:0x00007f5a90527a00>