Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (4) Show 4 proteins XML

Show more...Show more...Show more...Show more...

Record Information

Version

5.0

Status

Expected but not Quantified

Creation Date

2005-11-16 15:48:42 UTC

Update Date

2021-09-14 15:44:40 UTC

HMDB ID

HMDB0001351

Secondary Accession Numbers

HMDB01351

Metabolite Identification

Common Name

Deoxyribose 1-phosphate

Description

Deoxyribose 1-phosphate belongs to the class of organic compounds known as pentoses. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms. A Deoxyribose 1-phosphate with D-ribofuranose as the sugar. Deoxyribose 1-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). Deoxyribose 1-phosphate exists in all living species, ranging from bacteria to humans.

Structure

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

  Mrv0541 02231219042D          

 13 13  0  0  1  0            999 V2000
    0.0984   -0.0037    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -0.5714    0.4730    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.1552   -0.7946    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    0.8816    0.2535    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -1.2335   -0.0037    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
   -0.9839   -0.7946    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    1.7028    0.2535    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
   -2.0131    0.2535    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   -1.4682   -1.4568    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.5239    0.2535    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990    1.0785    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    1.6990   -0.5676    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -2.1834    1.0595    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  0  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>
HMDB0001351

> <DATABASE_NAME>
hmdb

> <SMILES>
OC[C@H]1OC(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-PYHARJCCSA-N

> <FORMULA>
C5H11O7P

> <MOLECULAR_WEIGHT>
214.1104

> <EXACT_MASS>
214.024239218

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
17.207710029989737

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(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>
deoxyribose-1-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 23-FEB-12   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   23-FEB-12         0                                  
HETATM    1  C   UNK     0       0.184  -0.007   0.000  0.00  0.00           C+0
HETATM    2  O   UNK     0      -1.067   0.883   0.000  0.00  0.00           O+0
HETATM    3  C   UNK     0      -0.290  -1.483   0.000  0.00  0.00           C+0
HETATM    4  O   UNK     0       1.646   0.473   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0      -2.303  -0.007   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0      -1.837  -1.483   0.000  0.00  0.00           C+0
HETATM    7  P   UNK     0       3.179   0.473   0.000  0.00  0.00           P+0
HETATM    8  C   UNK     0      -3.758   0.473   0.000  0.00  0.00           C+0
HETATM    9  O   UNK     0      -2.741  -2.719   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       4.711   0.473   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       3.171   2.013   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0       3.171  -1.060   0.000  0.00  0.00           O+0
HETATM   13  O   UNK     0      -4.076   1.978   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

View in JSmol View Stereo Labels

Synonyms

Value	Source
2-Deoxy-1-O-phosphono-D-erythro-pentofuranose	ChEBI
2-Deoxy-1-O-phosphono-D-ribofuranose	ChEBI
2-Deoxy-D-ribose 1-phosphate	ChEBI
2-Deoxy-D-ribose 1-phosphoric acid	Generator
Deoxyribose 1-phosphoric acid	Generator
2-Deoxy-alpha-D-ribose 1-phosphate	HMDB
2-Deoxy-alpha-delta-ribose 1-phosphate	HMDB
2-Deoxy-D-erythro-pentofuranose 1-phosphate	HMDB
2-Deoxy-D-ribose-1-phosphate	HMDB
2-Deoxy-delta-erythro-pentofuranose 1-phosphate	HMDB
2-Deoxy-delta-ribose 1-phosphate	HMDB
2-Deoxy-delta-ribose-1-phosphate	HMDB
2-Deoxyribofuranose 1-phosphate	HMDB
D-2-Deoxy-ribofuranose 1-phosphate	HMDB
delta-2-Deoxy-ribofuranose 1-phosphate	HMDB
Deoxyribose-1-phosphate	HMDB
2-Deoxyribose 1-phosphate	HMDB
2-Deoxyribose 1-phosphate, (alpha-D-erythro)-isomer	HMDB
2-Deoxyribose 1-phosphate, (beta-D-erythro)-isomer	HMDB

Chemical Formula

C₅H₁₁O₇P

Average Molecular Weight

214.1104

Monoisotopic Molecular Weight

214.024239218

IUPAC Name

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

Traditional Name

deoxyribose-1-phosphate

CAS Registry Number

17210-42-3

SMILES

OC[C@H]1OC(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-PYHARJCCSA-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-deoxyribose 1-phosphate (CHEBI:28542 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Cytoplasm (HMDB: HMDB0001351)

Source

Endogenous

Endogenous (HMDB: HMDB0001351)

Pheasant (FooDB: FOOD00430)
Squab (FooDB: FOOD00481)
Turkey (FooDB: FOOD00494)
Quail (FooDB: FOOD00541)
Anatidae (FooDB: FOOD00576)
Rock ptarmigan (FooDB: FOOD00597)
Columbidae (Dove, Pigeon) (FooDB: FOOD00610)
Chicken (FooDB: FOOD00329)
Mallard duck (FooDB: FOOD00353)
Emu (FooDB: FOOD00360)
Greylag goose (FooDB: FOOD00368)
Guinea hen (FooDB: FOOD00373)
Ostrich (FooDB: FOOD00422)
Velvet duck (FooDB: FOOD00427)

Lagomorph

Ovis

Sheep (Mutton, Lamb) (FooDB: FOOD00473)

Bovine

Venison

Deer (FooDB: FOOD00524)
Mule deer (FooDB: FOOD00348)
Elk (FooDB: FOOD00359)

Caprae

Domestic goat (FooDB: FOOD00529)

Swine

Domestic pig (FooDB: FOOD00536)
Wild boar (FooDB: FOOD00307)

Equine

Horse (FooDB: FOOD00378)

Process

Naturally occurring process

Biological process

Biochemical pathway

Drug action pathway

Thioguanine Action Pathway (HMDB: HMDB0001351)
Azathioprine Action Pathway (PathBank: SMP0000427)
Mercaptopurine Action Pathway (PathBank: SMP0000428)
Thioguanine Action Pathway (PathBank: SMP0000430)

Metabolic pathway

Pyrimidine Metabolism (PathBank: SMP0087340)
Purine Metabolism (PathBank: SMP0063668)
Pentose Phosphate Pathway (PathBank: SMP0087246)
Pentose Phosphate Pathway (HMDB: HMDB0001351)
Salvage Pathways of Pyrimidine Deoxyribonucleotides (PathBank: SMP0002073)
Pyrimidine Deoxyribonucleosides Degradation (PathBank: SMP0002075)
Purine Deoxyribonucleosides Degradation (PathBank: SMP0002089)

Disease pathway

Xanthinuria Type II (PathBank: SMP0120578)
Beta-Ureidopropionase Deficiency (PathBank: SMP0120678)
Gout or Kelley-Seegmiller Syndrome (PathBank: SMP0120709)
Xanthine Dehydrogenase Deficiency (Xanthinuria) (PathBank: SMP0120717)
Transaldolase Deficiency (PathBank: SMP0120804)
Mitochondrial DNA Depletion Syndrome (PathBank: SMP0120820)
UMP Synthase Deficiency (Orotic Aciduria) (PathBank: SMP0120507)
Adenylosuccinate Lyase Deficiency (PathBank: SMP0120670)
AICA-Ribosiduria (PathBank: SMP0120673)
Purine Nucleoside Phosphorylase Deficiency (PathBank: SMP0120756)
Adenine Phosphoribosyltransferase Deficiency (APRT) (PathBank: SMP0120819)
Myoadenylate Deaminase Deficiency (PathBank: SMP0120821)
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy) (HMDB: HMDB0001351)
Adenosine Deaminase Deficiency (PathBank: SMP0120448)
Dihydropyrimidinase Deficiency (PathBank: SMP0120473)
Lesch-Nyhan Syndrome (LNS) (PathBank: SMP0120508)
Glucose-6-phosphate Dehydrogenase Deficiency (PathBank: SMP0120583)
Molybdenum Cofactor Deficiency (PathBank: SMP0120752)
Ribose-5-phosphate Isomerase Deficiency (PathBank: SMP0120803)
MNGIE (Mitochondrial Neurogastrointestinal Encephalopathy) (PathBank: SMP0120530)
Xanthinuria Type I (PathBank: SMP0120577)
Mitochondrial DNA Depletion Syndrome (PathBank: SMP0000536)

Role

Not Available

Physical Properties

State

Solid

Experimental Molecular Properties

Property	Value	Reference
Melting Point	Not Available	Not Available
Boiling Point	Not Available	Not Available
Water Solubility	Not Available	Not Available
LogP	Not Available	Not Available

Experimental Chromatographic Properties

Not Available

Predicted Molecular 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	17.21 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

Predicted Chromatographic Properties

Predicted Collision Cross Sections

Predictor	Adduct Type	CCS Value (Å²)	Reference
DarkChem	[M+H]+	148.095	31661259
DarkChem	[M-H]-	141.385	31661259
AllCCS	[M+H]+	146.589	32859911
AllCCS	[M-H]-	138.197	32859911
DeepCCS	[M+H]+	128.597	30932474
DeepCCS	[M-H]-	126.201	30932474
DeepCCS	[M-2H]-	160.618	30932474
DeepCCS	[M+Na]+	136.116	30932474
AllCCS	[M+H]+	146.6	32859911
AllCCS	[M+H-H2O]+	142.7	32859911
AllCCS	[M+NH4]+	150.2	32859911
AllCCS	[M+Na]+	151.3	32859911
AllCCS	[M-H]-	138.2	32859911
AllCCS	[M+Na-2H]-	139.1	32859911
AllCCS	[M+HCOO]-	140.1	32859911

Predicted Kovats Retention Indices

Underivatized

Metabolite	SMILES	Kovats RI Value	Column Type	Reference
Deoxyribose 1-phosphate	OC[C@H]1OC(C[C@@H]1O)OP(O)(O)=O	2908.4	Standard polar	33892256
Deoxyribose 1-phosphate	OC[C@H]1OC(C[C@@H]1O)OP(O)(O)=O	1745.1	Standard non polar	33892256
Deoxyribose 1-phosphate	OC[C@H]1OC(C[C@@H]1O)OP(O)(O)=O	1851.7	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Deoxyribose 1-phosphate,1TMS,isomer #1	C[Si](C)(C)OC[C@H]1OC(OP(=O)(O)O)C[C@@H]1O	1921.6	Semi standard non polar	33892256
Deoxyribose 1-phosphate,1TMS,isomer #2	C[Si](C)(C)O[C@H]1CC(OP(=O)(O)O)O[C@@H]1CO	1916.1	Semi standard non polar	33892256
Deoxyribose 1-phosphate,1TMS,isomer #3	C[Si](C)(C)OP(=O)(O)OC1C[C@H](O)[C@@H](CO)O1	1893.8	Semi standard non polar	33892256
Deoxyribose 1-phosphate,2TMS,isomer #1	C[Si](C)(C)OC[C@H]1OC(OP(=O)(O)O)C[C@@H]1O[Si](C)(C)C	1937.6	Semi standard non polar	33892256
Deoxyribose 1-phosphate,2TMS,isomer #2	C[Si](C)(C)OC[C@H]1OC(OP(=O)(O)O[Si](C)(C)C)C[C@@H]1O	1958.7	Semi standard non polar	33892256
Deoxyribose 1-phosphate,2TMS,isomer #3	C[Si](C)(C)O[C@H]1CC(OP(=O)(O)O[Si](C)(C)C)O[C@@H]1CO	1945.4	Semi standard non polar	33892256
Deoxyribose 1-phosphate,2TMS,isomer #4	C[Si](C)(C)OP(=O)(OC1C[C@H](O)[C@@H](CO)O1)O[Si](C)(C)C	1890.0	Semi standard non polar	33892256
Deoxyribose 1-phosphate,3TMS,isomer #1	C[Si](C)(C)OC[C@H]1OC(OP(=O)(O)O[Si](C)(C)C)C[C@@H]1O[Si](C)(C)C	1962.6	Semi standard non polar	33892256
Deoxyribose 1-phosphate,3TMS,isomer #1	C[Si](C)(C)OC[C@H]1OC(OP(=O)(O)O[Si](C)(C)C)C[C@@H]1O[Si](C)(C)C	1920.3	Standard non polar	33892256
Deoxyribose 1-phosphate,3TMS,isomer #1	C[Si](C)(C)OC[C@H]1OC(OP(=O)(O)O[Si](C)(C)C)C[C@@H]1O[Si](C)(C)C	2412.0	Standard polar	33892256
Deoxyribose 1-phosphate,3TMS,isomer #2	C[Si](C)(C)OC[C@H]1OC(OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C[C@@H]1O	1951.0	Semi standard non polar	33892256
Deoxyribose 1-phosphate,3TMS,isomer #2	C[Si](C)(C)OC[C@H]1OC(OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C[C@@H]1O	2001.0	Standard non polar	33892256
Deoxyribose 1-phosphate,3TMS,isomer #2	C[Si](C)(C)OC[C@H]1OC(OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C[C@@H]1O	2336.7	Standard polar	33892256
Deoxyribose 1-phosphate,3TMS,isomer #3	C[Si](C)(C)O[C@H]1CC(OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[C@@H]1CO	1933.8	Semi standard non polar	33892256
Deoxyribose 1-phosphate,3TMS,isomer #3	C[Si](C)(C)O[C@H]1CC(OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[C@@H]1CO	1937.1	Standard non polar	33892256
Deoxyribose 1-phosphate,3TMS,isomer #3	C[Si](C)(C)O[C@H]1CC(OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O[C@@H]1CO	2216.5	Standard polar	33892256
Deoxyribose 1-phosphate,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1OC(OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C[C@@H]1O[Si](C)(C)C	1952.1	Semi standard non polar	33892256
Deoxyribose 1-phosphate,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1OC(OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C[C@@H]1O[Si](C)(C)C	1976.2	Standard non polar	33892256
Deoxyribose 1-phosphate,4TMS,isomer #1	C[Si](C)(C)OC[C@H]1OC(OP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)C[C@@H]1O[Si](C)(C)C	2144.8	Standard polar	33892256
Deoxyribose 1-phosphate,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1OC(OP(=O)(O)O)C[C@@H]1O	2159.8	Semi standard non polar	33892256
Deoxyribose 1-phosphate,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1CC(OP(=O)(O)O)O[C@@H]1CO	2163.1	Semi standard non polar	33892256
Deoxyribose 1-phosphate,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OP(=O)(O)OC1C[C@H](O)[C@@H](CO)O1	2134.4	Semi standard non polar	33892256
Deoxyribose 1-phosphate,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1OC(OP(=O)(O)O)C[C@@H]1O[Si](C)(C)C(C)(C)C	2374.6	Semi standard non polar	33892256
Deoxyribose 1-phosphate,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1OC(OP(=O)(O)O[Si](C)(C)C(C)(C)C)C[C@@H]1O	2386.1	Semi standard non polar	33892256
Deoxyribose 1-phosphate,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1CC(OP(=O)(O)O[Si](C)(C)C(C)(C)C)O[C@@H]1CO	2374.9	Semi standard non polar	33892256
Deoxyribose 1-phosphate,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OP(=O)(OC1C[C@H](O)[C@@H](CO)O1)O[Si](C)(C)C(C)(C)C	2333.2	Semi standard non polar	33892256
Deoxyribose 1-phosphate,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1OC(OP(=O)(O)O[Si](C)(C)C(C)(C)C)C[C@@H]1O[Si](C)(C)C(C)(C)C	2616.5	Semi standard non polar	33892256
Deoxyribose 1-phosphate,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1OC(OP(=O)(O)O[Si](C)(C)C(C)(C)C)C[C@@H]1O[Si](C)(C)C(C)(C)C	2513.5	Standard non polar	33892256
Deoxyribose 1-phosphate,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1OC(OP(=O)(O)O[Si](C)(C)C(C)(C)C)C[C@@H]1O[Si](C)(C)C(C)(C)C	2700.6	Standard polar	33892256
Deoxyribose 1-phosphate,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1OC(OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C[C@@H]1O	2590.3	Semi standard non polar	33892256
Deoxyribose 1-phosphate,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1OC(OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C[C@@H]1O	2588.9	Standard non polar	33892256
Deoxyribose 1-phosphate,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)OC[C@H]1OC(OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C[C@@H]1O	2643.7	Standard polar	33892256
Deoxyribose 1-phosphate,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1CC(OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O[C@@H]1CO	2588.7	Semi standard non polar	33892256
Deoxyribose 1-phosphate,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1CC(OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O[C@@H]1CO	2513.1	Standard non polar	33892256
Deoxyribose 1-phosphate,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1CC(OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O[C@@H]1CO	2535.4	Standard polar	33892256
Deoxyribose 1-phosphate,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1OC(OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C[C@@H]1O[Si](C)(C)C(C)(C)C	2781.3	Semi standard non polar	33892256
Deoxyribose 1-phosphate,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1OC(OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C[C@@H]1O[Si](C)(C)C(C)(C)C	2657.3	Standard non polar	33892256
Deoxyribose 1-phosphate,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)OC[C@H]1OC(OP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)C[C@@H]1O[Si](C)(C)C(C)(C)C	2560.1	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Deoxyribose 1-phosphate GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9100000000-0b83a26b67c41b7ca8c9	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Deoxyribose 1-phosphate GC-MS (2 TMS) - 70eV, Positive	splash10-0002-9120000000-ed5a733798dcf4d7c439	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Deoxyribose 1-phosphate GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	Wishart Lab	View Spectrum

MS/MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 1-phosphate 10V, Positive-QTOF	splash10-00kb-9430000000-ef11f7c98a651dbe59d7	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 1-phosphate 20V, Positive-QTOF	splash10-0002-9400000000-5e3754bb21aff6c3ce06	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 1-phosphate 40V, Positive-QTOF	splash10-0002-9300000000-615ca1fa907e42aa9c9d	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 1-phosphate 10V, Negative-QTOF	splash10-03fs-9260000000-5a7b6b1faaba56e1c97d	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 1-phosphate 20V, Negative-QTOF	splash10-004i-9100000000-5f0b0b093f8d726f7076	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 1-phosphate 40V, Negative-QTOF	splash10-004i-9000000000-b1cd1b026728c07d36bb	2015-09-15	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 1-phosphate 10V, Positive-QTOF	splash10-014i-3690000000-41b666017994305912b8	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 1-phosphate 20V, Positive-QTOF	splash10-0002-9200000000-99440f284bdeb59e2f04	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 1-phosphate 40V, Positive-QTOF	splash10-052b-9000000000-f613851350f97d5430bc	2021-09-22	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 1-phosphate 10V, Negative-QTOF	splash10-03fr-9080000000-e66a31856a5562cb0b9d	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 1-phosphate 20V, Negative-QTOF	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 1-phosphate 40V, Negative-QTOF	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-25	Wishart Lab	View Spectrum

NMR Spectra

Spectrum Type	Description	Deposition Date	Source	View
Predicted 1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)	2022-08-18	Wishart Lab	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm (predicted from logP)

Biospecimen Locations

Not Available

Tissue Locations

Not Available

Pathways

Name	SMPDB/PathBank	KEGG
Pyrimidine metabolism	Not Available
pentose phosphate pathway	Not Available	Not Available
Glucose-6-phosphate dehydrogenase deficiency		Not Available
Ribose-5-phosphate isomerase deficiency		Not Available
Transaldolase deficiency		Not Available

Normal Concentrations

Not Available

Abnormal Concentrations

Not Available

Associated Disorders and Diseases

Disease References

None

Associated OMIM IDs

None

External Links

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB022571

KNApSAcK ID

Not Available

Chemspider ID

388420

KEGG Compound ID

C00672

BioCyc ID

Not Available

BiGG ID

35664

Wikipedia Link

Not Available

METLIN ID

6182

PubChem Compound

439287

PDB ID

Not Available

ChEBI ID

28542

Food Biomarker Ontology

Not Available

VMH ID

2DR1P

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Not Available

Material Safety Data Sheet (MSDS)

Not Available

General References

Holmberg I, Stal P, Hamberg M: Quantitative determination of 8-hydroxy-2'-deoxyguanosine in human urine by isotope dilution mass spectrometry: normal levels in hemochromatosis. Free Radic Biol Med. 1999 Jan;26(1-2):129-35. [PubMed:9890648 ]

Enzymes

Enzyme Details

1. Ribokinase

General function:: Involved in ribokinase activity
Specific function:: Not Available
Gene Name:: RBKS
Uniprot ID:: Q9H477
Molecular weight:: 34142.685

Enzyme Details

2. Phosphoglucomutase-2

General function:: Involved in intramolecular transferase activity, phosphotransferases
Specific function:: Catalyzes the conversion of the nucleoside breakdown products ribose-1-phosphate and deoxyribose-1-phosphate to the corresponding 5-phosphopentoses. May also catalyze the interconversion of glucose-1-phosphate and glucose-6-phosphate. Has low glucose 1,6-bisphosphate synthase activity.
Gene Name:: PGM2
Uniprot ID:: Q96G03
Molecular weight:: 68282.765

Reactions

Deoxyribose 1-phosphate → Deoxyribose 5-phosphate	details
Deoxyribose 1-phosphate → Deoxyribose 5-monophosphate	details

Enzyme Details

3. Purine nucleoside phosphorylase

General function:: Involved in purine-nucleoside phosphorylase activity
Specific function:: The purine nucleoside phosphorylases catalyze the phosphorolytic breakdown of the N-glycosidic bond in the beta-(deoxy)ribonucleoside molecules, with the formation of the corresponding free purine bases and pentose-1-phosphate.
Gene Name:: PNP
Uniprot ID:: P00491
Molecular weight:: 32117.69

Reactions

Deoxyguanosine + Phosphate → Guanine + Deoxyribose 1-phosphate	details
Deoxyuridine + Phosphate → Uracil + Deoxyribose 1-phosphate	details
Deoxyadenosine + Phosphate → Adenine + Deoxyribose 1-phosphate	details
Deoxyinosine + Phosphate → Hypoxanthine + Deoxyribose 1-phosphate	details

Enzyme Details

4. Thymidine phosphorylase

General function:: Involved in transferase activity, transferring glycosyl groups
Specific function:: May have a role in maintaining the integrity of the blood vessels. Has growth promoting activity on endothelial cells, angiogenic activity in vivo and chemotactic activity on endothelial cells in vitro. Catalyzes the reversible phosphorolysis of thymidine. The produced molecules are then utilized as carbon and energy sources or in the rescue of pyrimidine bases for nucleotide synthesis.
Gene Name:: TYMP
Uniprot ID:: P19971
Molecular weight:: 49954.965

Reactions

Thymidine + Phosphate → Thymine + Deoxyribose 1-phosphate	details
Deoxyuridine + Phosphate → Uracil + Deoxyribose 1-phosphate	details
Fluorouracil + Deoxyribose 1-phosphate → Floxuridine + Phosphate	details

Showing metabocard for Deoxyribose 1-phosphate (HMDB0001351)

MOL for HMDB0001351 (Deoxyribose 1-phosphate)

3D MOL for HMDB0001351 (Deoxyribose 1-phosphate)

3D SDF for HMDB0001351 (Deoxyribose 1-phosphate)

3D-SDF for HMDB0001351 (Deoxyribose 1-phosphate)

PDB for HMDB0001351 (Deoxyribose 1-phosphate)

3D PDB for HMDB0001351 (Deoxyribose 1-phosphate)

SMILES for HMDB0001351 (Deoxyribose 1-phosphate)

INCHI for HMDB0001351 (Deoxyribose 1-phosphate)

Structure for HMDB0001351 (Deoxyribose 1-phosphate)

3D Structure for HMDB0001351 (Deoxyribose 1-phosphate)

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions

Reactions

Reactions