Jump To Section:

Identification Taxonomy Ontology Physical properties Spectra Biological properties Concentrations Links References enzymes (3) Show 3 proteins XML

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 15:19:06 UTC

HMDB ID

HMDB0001031

Secondary Accession Numbers

HMDB01031

Metabolite Identification

Common Name

Deoxyribose 5-phosphate

Description

Deoxyribose 5-phosphate is a a metabolite in the pentose phosphate pathway. It can be generated from D-glyceraldehdye-3 phosphate via the enzyme 2-Deoxyribose 5-phosphate aldolase (DERA). Alternately Deoxyribose 5-phosphate can be converted to D-glyceraldehyde-3 phosphate that can then feed into the pentose phosphate pathway. Deoxyribose 5-phosphate can also be generated from 2-Deoxy-D-ribose via the enzyme Ribokinase (EC 2.7.1.15). It has been shown in a number of organisms that deoxynucleosides or deoxyriboses cause the induction of aldolases (such as DERA) involved in their catabolism, leading to the utilisation of the pentose moiety as carbon and energy source.

Structure

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

  Mrv0541 02231218532D          

 13 13  0  0  1  0            999 V2000
   10.8915   -9.1538    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    9.1458   -7.9250    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   10.0709   -9.0675    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    9.8994   -8.2605    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   11.2270   -8.4001    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    9.5189   -9.6806    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   12.0340   -8.2286    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.6414   -6.0153    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.9703   -7.5226    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    7.5522   -6.4334    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    9.0595   -7.1045    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   10.6139   -7.8480    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    8.3059   -6.7690    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  1  3  1  0  0  0  0
  1  5  1  0  0  0  0
  4  2  1  1  0  0  0
  2 11  1  0  0  0  0
  3  6  1  6  0  0  0
  3  4  1  0  0  0  0
  4 12  1  0  0  0  0
  5  7  1  1  0  0  0
  5 12  1  0  0  0  0
  8 13  1  0  0  0  0
  9 13  1  0  0  0  0
 10 13  2  0  0  0  0
 11 13  1  0  0  0  0
M  END
> <DATABASE_ID>
HMDB0001031

> <DATABASE_NAME>
hmdb

> <SMILES>
O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1

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

> <INCHI_KEY>
KKZFLSZAWCYPOC-VPENINKCSA-N

> <FORMULA>
C5H11O7P

> <MOLECULAR_WEIGHT>
214.1104

> <EXACT_MASS>
214.024239218

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
17.46469128826616

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3S,5R)-3,5-dihydroxyoxolan-2-yl]methoxy}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>
6.255762605408527

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.2299449119892785

> <JCHEM_PKA_STRONGEST_BASIC>
-3.2560418070675405

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
39.3231

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.75e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
deoxyribose-5-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      20.331 -17.087   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0      17.072 -14.793   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0      18.799 -16.926   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      18.479 -15.420   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0      20.957 -15.680   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0      17.769 -18.070   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      22.463 -15.360   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0      16.131 -11.229   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      14.878 -14.042   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0      14.097 -12.009   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0      16.911 -13.262   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      19.813 -14.650   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0      15.504 -12.635   0.000  0.00  0.00           P+0
CONECT    1    3    5                                                       
CONECT    2    4   11                                                       
CONECT    3    1    6    4                                                  
CONECT    4    2    3   12                                                  
CONECT    5    1    7   12                                                  
CONECT    6    3                                                            
CONECT    7    5                                                            
CONECT    8   13                                                            
CONECT    9   13                                                            
CONECT   10   13                                                            
CONECT   11    2   13                                                       
CONECT   12    4    5                                                       
CONECT   13    8    9   10   11                                             
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

View in JSmol View NMR Assignments View Stereo Labels

Synonyms

Value	Source
Deoxyribose 5-phosphoric acid	Generator
2-Deoxy-alpha-D-ribose 5-phosphate	HMDB
2-Deoxy-alpha-delta-ribose 5-phosphate	HMDB
2-Deoxy-D-ribose 5-phosphate	HMDB
2-Deoxy-D-ribose-5-phosphate	HMDB
2-Deoxyribose 5-phosphate	HMDB
2-Deoxyribose-5-p	HMDB
2-Deoxyribose-5-phosphate	HMDB
Deoxy-ribose-5P	HMDB
Deoxyribose-5-p	HMDB
Deoxyribose-5-phosphate	HMDB

Chemical Formula

C₅H₁₁O₇P

Average Molecular Weight

214.1104

Monoisotopic Molecular Weight

214.024239218

IUPAC Name

{[(2R,3S,5R)-3,5-dihydroxyoxolan-2-yl]methoxy}phosphonic acid

Traditional Name

deoxyribose-5-phosphate

CAS Registry Number

102916-66-5

SMILES

O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1

InChI Identifier

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

InChI Key

KKZFLSZAWCYPOC-VPENINKCSA-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 phosphate
Monosaccharide phosphate
Monoalkyl phosphate
Alkyl phosphate
Phosphoric acid ester
Organic phosphoric acid derivative
Tetrahydrofuran
Secondary alcohol
Hemiacetal
Oxacycle
Organoheterocyclic compound
Organic oxide
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

2-deoxy-D-ribofuranose 5-phosphate (CHEBI:40923 )

Ontology

Physiological effect

Not Available

Disposition

Biological location

Cellular substructure

Cytoplasm (HMDB: HMDB0001031)

Source

Endogenous

Endogenous (HMDB: HMDB0001031)

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

Disease pathway

Transaldolase Deficiency (PathBank: SMP0120804)
Glucose-6-phosphate Dehydrogenase Deficiency (PathBank: SMP0120583)
Ribose-5-phosphate Isomerase Deficiency (PathBank: SMP0120803)

Metabolic pathway

Pentose Phosphate Pathway (PathBank: SMP0087246)
Pentose Phosphate Pathway (HMDB: HMDB0001031)
Purine Deoxyribonucleosides Degradation (PathBank: SMP0002089)

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

Experimental Collision Cross Sections

Adduct Type	Data Source	CCS Value (Å²)	Reference
[M-H]-	Not Available	132.469	http://allccs.zhulab.cn/database/detail?ID=AllCCS00000382

Predicted Molecular Properties

Property	Value	Source
Water Solubility	37.5 g/L	ALOGPS
logP	-2.1	ALOGPS
logP	-1.5	ChemAxon
logS	-0.76	ALOGPS
pKa (Strongest Acidic)	1.23	ChemAxon
pKa (Strongest Basic)	-3.3	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	17.46 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]+	146.836	31661259
DarkChem	[M-H]-	141.06	31661259
AllCCS	[M+H]+	146.26	32859911
AllCCS	[M-H]-	138.191	32859911
DeepCCS	[M+H]+	138.53	30932474
DeepCCS	[M-H]-	136.157	30932474
DeepCCS	[M-2H]-	169.846	30932474
DeepCCS	[M+Na]+	144.454	30932474
AllCCS	[M+H]+	146.3	32859911
AllCCS	[M+H-H2O]+	142.4	32859911
AllCCS	[M+NH4]+	149.9	32859911
AllCCS	[M+Na]+	150.9	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 5-phosphate	O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1	2938.8	Standard polar	33892256
Deoxyribose 5-phosphate	O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1	1723.0	Standard non polar	33892256
Deoxyribose 5-phosphate	O[C@H]1C[C@H](O)[C@@H](COP(O)(O)=O)O1	1877.6	Semi standard non polar	33892256

Derivatized

Derivative Name / Structure	SMILES	Kovats RI Value	Column Type	Reference
Deoxyribose 5-phosphate,1TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O)O)O1	1922.0	Semi standard non polar	33892256
Deoxyribose 5-phosphate,1TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O)O	1894.2	Semi standard non polar	33892256
Deoxyribose 5-phosphate,1TMS,isomer #3	C[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H](O)C[C@@H]1O	1913.5	Semi standard non polar	33892256
Deoxyribose 5-phosphate,2TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O)O)O1	1923.7	Semi standard non polar	33892256
Deoxyribose 5-phosphate,2TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O)O[Si](C)(C)C)O1	1976.1	Semi standard non polar	33892256
Deoxyribose 5-phosphate,2TMS,isomer #3	C[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C	1965.2	Semi standard non polar	33892256
Deoxyribose 5-phosphate,2TMS,isomer #4	C[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](O)C[C@@H]1O)O[Si](C)(C)C	1942.4	Semi standard non polar	33892256
Deoxyribose 5-phosphate,3TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O)O[Si](C)(C)C)O1	1970.5	Semi standard non polar	33892256
Deoxyribose 5-phosphate,3TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O)O[Si](C)(C)C)O1	1946.9	Standard non polar	33892256
Deoxyribose 5-phosphate,3TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O)O[Si](C)(C)C)O1	2431.5	Standard polar	33892256
Deoxyribose 5-phosphate,3TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O1	2011.9	Semi standard non polar	33892256
Deoxyribose 5-phosphate,3TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O1	1979.0	Standard non polar	33892256
Deoxyribose 5-phosphate,3TMS,isomer #2	C[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O1	2244.6	Standard polar	33892256
Deoxyribose 5-phosphate,3TMS,isomer #3	C[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	2011.9	Semi standard non polar	33892256
Deoxyribose 5-phosphate,3TMS,isomer #3	C[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	1966.1	Standard non polar	33892256
Deoxyribose 5-phosphate,3TMS,isomer #3	C[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C	2212.8	Standard polar	33892256
Deoxyribose 5-phosphate,4TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O1	1990.4	Semi standard non polar	33892256
Deoxyribose 5-phosphate,4TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O1	1983.8	Standard non polar	33892256
Deoxyribose 5-phosphate,4TMS,isomer #1	C[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C)[C@@H](COP(=O)(O[Si](C)(C)C)O[Si](C)(C)C)O1	2143.8	Standard polar	33892256
Deoxyribose 5-phosphate,1TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O)O)O1	2162.8	Semi standard non polar	33892256
Deoxyribose 5-phosphate,1TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O)O	2148.4	Semi standard non polar	33892256
Deoxyribose 5-phosphate,1TBDMS,isomer #3	CC(C)(C)[Si](C)(C)OP(=O)(O)OC[C@H]1O[C@@H](O)C[C@@H]1O	2161.4	Semi standard non polar	33892256
Deoxyribose 5-phosphate,2TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O)O)O1	2351.2	Semi standard non polar	33892256
Deoxyribose 5-phosphate,2TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)O1	2414.5	Semi standard non polar	33892256
Deoxyribose 5-phosphate,2TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O)O[Si](C)(C)C(C)(C)C	2412.0	Semi standard non polar	33892256
Deoxyribose 5-phosphate,2TBDMS,isomer #4	CC(C)(C)[Si](C)(C)OP(=O)(OC[C@H]1O[C@@H](O)C[C@@H]1O)O[Si](C)(C)C(C)(C)C	2395.3	Semi standard non polar	33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)O1	2613.5	Semi standard non polar	33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)O1	2543.6	Standard non polar	33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O)O[Si](C)(C)C(C)(C)C)O1	2692.8	Standard polar	33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O1	2625.3	Semi standard non polar	33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O1	2548.2	Standard non polar	33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #2	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)[C@@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O1	2567.2	Standard polar	33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2632.6	Semi standard non polar	33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2548.2	Standard non polar	33892256
Deoxyribose 5-phosphate,3TBDMS,isomer #3	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O)O[C@@H]1COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C	2540.0	Standard polar	33892256
Deoxyribose 5-phosphate,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O1	2831.0	Semi standard non polar	33892256
Deoxyribose 5-phosphate,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O1	2665.4	Standard non polar	33892256
Deoxyribose 5-phosphate,4TBDMS,isomer #1	CC(C)(C)[Si](C)(C)O[C@H]1C[C@H](O[Si](C)(C)C(C)(C)C)[C@@H](COP(=O)(O[Si](C)(C)C(C)(C)C)O[Si](C)(C)C(C)(C)C)O1	2551.5	Standard polar	33892256

Spectra

GC-MS Spectra

Spectrum Type	Description	Splash Key	Deposition Date	Source	View
Predicted GC-MS	Predicted GC-MS Spectrum - Deoxyribose 5-phosphate GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9600000000-bdc9f54852e365293f11	2016-09-22	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Deoxyribose 5-phosphate GC-MS (2 TMS) - 70eV, Positive	splash10-006x-9185000000-bfea5991ff0a9475e0b9	2017-10-06	Wishart Lab	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - Deoxyribose 5-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 5-phosphate 10V, Positive-QTOF	splash10-014i-3970000000-30d79004fa4e6fa5906d	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 5-phosphate 20V, Positive-QTOF	splash10-00kb-7910000000-3de23781c803b806a189	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 5-phosphate 40V, Positive-QTOF	splash10-052b-9100000000-25bca847c2e30ed7e327	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 5-phosphate 10V, Negative-QTOF	splash10-03fr-8490000000-6979c10cf3fafe02069d	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 5-phosphate 20V, Negative-QTOF	splash10-004i-9100000000-43a8b73209f01319d3c2	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 5-phosphate 40V, Negative-QTOF	splash10-004i-9000000000-16fc473b541d2a247daf	2016-09-12	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 5-phosphate 10V, Positive-QTOF	splash10-014j-8910000000-7c465e8be120df2e083a	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 5-phosphate 20V, Positive-QTOF	splash10-00r2-9200000000-4f0c0c2bf45b1986dd6a	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 5-phosphate 40V, Positive-QTOF	splash10-0002-9100000000-a91ae5a4e7423371ee52	2021-09-23	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 5-phosphate 10V, Negative-QTOF	splash10-01r2-9030000000-5eb77e97817ae8e3e50f	2021-09-25	Wishart Lab	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - Deoxyribose 5-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 5-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, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	Wishart Lab	View Spectrum
Predicted 1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)	2021-09-16	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
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

FDB022380

KNApSAcK ID

Not Available

Chemspider ID

25057464

KEGG Compound ID

C00673

BioCyc ID

Not Available

BiGG ID

35666

Wikipedia Link

Not Available

METLIN ID

PubChem Compound

PDB ID

ChEBI ID

Food Biomarker Ontology

Not Available

VMH ID

2DR5P

MarkerDB ID

Not Available

Good Scents ID

Not Available

References

Synthesis Reference

Method of preparing 2-deoxyribose 5-phosphate US Patent #7270992

Material Safety Data Sheet (MSDS)

Download (PDF)

General References

Not Available

Enzymes

Enzyme Details

1. Putative deoxyribose-phosphate aldolase

General function:: Involved in catalytic activity
Specific function:: Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate (By similarity).
Gene Name:: DERA
Uniprot ID:: Q9Y315
Molecular weight:: 35230.395

Enzyme Details

2. Ribokinase

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

Enzyme Details

3. 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

Showing metabocard for Deoxyribose 5-phosphate (HMDB0001031)

MOL for HMDB0001031 (Deoxyribose 5-phosphate)

3D MOL for HMDB0001031 (Deoxyribose 5-phosphate)

3D SDF for HMDB0001031 (Deoxyribose 5-phosphate)

3D-SDF for HMDB0001031 (Deoxyribose 5-phosphate)

PDB for HMDB0001031 (Deoxyribose 5-phosphate)

3D PDB for HMDB0001031 (Deoxyribose 5-phosphate)

SMILES for HMDB0001031 (Deoxyribose 5-phosphate)

INCHI for HMDB0001031 (Deoxyribose 5-phosphate)

Structure for HMDB0001031 (Deoxyribose 5-phosphate)

3D Structure for HMDB0001031 (Deoxyribose 5-phosphate)

Experimental Collision Cross Sections

Predicted Collision Cross Sections

Predicted Kovats Retention Indices

Underivatized

Derivatized

GC-MS Spectra

MS/MS Spectra

NMR Spectra

Enzymes

Reactions