MiMeDB: Showing metabocard for 5-Deoxyribose-1-phosphate (MMDBc0052117)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-05-16 20:46:20 UTC

Update Date

2022-09-01 02:18:39 UTC

Metabolite ID

MMDBc0052117

Metabolite Identification

Common Name

5-Deoxyribose-1-phosphate

Description

5-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. 5-Deoxyribose-1-phosphate is an extremely weak basic (essentially neutral) compound (based on its pKa). 5-Deoxyribose-1-phosphate exists in all living organisms, ranging from bacteria to humans. fluorouracil and 5-deoxyribose-1-phosphate can be biosynthesized from 5'-deoxy-5-fluorouridine; which is catalyzed by the enzyme thymidine phosphorylase. In humans, 5-deoxyribose-1-phosphate is involved in capecitabine action pathway. These are monosaccharides in which the carbohydrate moiety contains five carbon atoms.

Structure

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


  Mrv0541 05161317592D          

 13 13  0  0  0  0            999 V2000
    2.0198    0.8843    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    1.2352    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.1143    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
   -0.0997    0.6294    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.1553   -0.1553    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    0.5678    1.9393    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.8843    0.8843    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.3415   -2.3300    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.7478   -1.9119    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.7596   -1.2408    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.9803   -0.1553    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   -0.3297   -0.8227    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    0.0059   -1.5764    0.0000 P   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  3  2  1  0  0  0  0
  4  3  1  0  0  0  0
  5  4  1  0  0  0  0
  3  6  1  6  0  0  0
  4  7  1  6  0  0  0
 11  2  1  0  0  0  0
 11  5  1  0  0  0  0
  5 12  1  6  0  0  0
 13  8  1  0  0  0  0
 13  9  1  0  0  0  0
 13 10  2  0  0  0  0
 13 12  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0052117

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H11O7P/c1-2-3(6)4(7)5(11-2)12-13(8,9)10/h2-7H,1H3,(H2,8,9,10)/t2-,3-,4-,5-/m1/s1

> <INCHI_KEY>
XXQFKXPJJNBLSU-TXICZTDVSA-N

> <FORMULA>
C5H11O7P

> <MOLECULAR_WEIGHT>
214.1104

> <EXACT_MASS>
214.024239218

> <JCHEM_ACCEPTOR_COUNT>
6

> <JCHEM_AVERAGE_POLARIZABILITY>
17.1242051971225

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
4

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
{[(2R,3R,4S,5R)-3,4-dihydroxy-5-methyloxolan-2-yl]oxy}phosphonic acid

> <ALOGPS_LOGP>
-1.51

> <JCHEM_LOGP>
-1.3788603406666664

> <ALOGPS_LOGS>
-0.76

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
1

> <JCHEM_PHYSIOLOGICAL_CHARGE>
-2

> <JCHEM_PKA>
6.219526154575139

> <JCHEM_PKA_STRONGEST_ACIDIC>
1.155981210696972

> <JCHEM_PKA_STRONGEST_BASIC>
-3.6437250332552598

> <JCHEM_POLAR_SURFACE_AREA>
116.45000000000002

> <JCHEM_REFRACTIVITY>
39.290099999999995

> <JCHEM_ROTATABLE_BOND_COUNT>
2

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
3.76e+01 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5-deoxyribose-1-phosphate

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 16-MAY-13   NONE
TITLE     NULL                                                        
COMPND    NULL                                                        
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   16-MAY-13         0                                  
HETATM    1  C   UNK     0       3.770   1.651   0.000  0.00  0.00           C+0
HETATM    2  C   UNK     0       2.306   1.175   0.000  0.00  0.00           C+0
HETATM    3  C   UNK     0       1.060   2.080   0.000  0.00  0.00           C+0
HETATM    4  C   UNK     0      -0.186   1.175   0.000  0.00  0.00           C+0
HETATM    5  C   UNK     0       0.290  -0.290   0.000  0.00  0.00           C+0
HETATM    6  O   UNK     0       1.060   3.620   0.000  0.00  0.00           O+0
HETATM    7  O   UNK     0      -1.651   1.651   0.000  0.00  0.00           O+0
HETATM    8  O   UNK     0       0.637  -4.349   0.000  0.00  0.00           O+0
HETATM    9  O   UNK     0      -1.396  -3.569   0.000  0.00  0.00           O+0
HETATM   10  O   UNK     0       1.418  -2.316   0.000  0.00  0.00           O+0
HETATM   11  O   UNK     0       1.830  -0.290   0.000  0.00  0.00           O+0
HETATM   12  O   UNK     0      -0.615  -1.536   0.000  0.00  0.00           O+0
HETATM   13  P   UNK     0       0.011  -2.943   0.000  0.00  0.00           P+0
CONECT    1    2                                                            
CONECT    2    1    3   11                                                  
CONECT    3    2    4    6                                                  
CONECT    4    3    5    7                                                  
CONECT    5    4   11   12                                                  
CONECT    6    3                                                            
CONECT    7    4                                                            
CONECT    8   13                                                            
CONECT    9   13                                                            
CONECT   10   13                                                            
CONECT   11    2    5                                                       
CONECT   12    5   13                                                       
CONECT   13    8    9   10   12                                             
MASTER        0    0    0    0    0    0    0    0   13    0   26    0
END

Synonyms

Value	Source
5-Deoxy-1-O-phosphono-alpha-D-ribofuranose	ChEBI
5-Deoxy-alpha-D-ribose-1-phosphate	ChEBI
5-Deoxy-1-O-phosphono-a-D-ribofuranose	Generator
5-Deoxy-1-O-phosphono-α-D-ribofuranose	Generator
5-Deoxy-a-D-ribose-1-phosphate	Generator
5-Deoxy-a-D-ribose-1-phosphoric acid	Generator
5-Deoxy-alpha-D-ribose-1-phosphoric acid	Generator
5-Deoxy-α-D-ribose-1-phosphate	Generator
5-Deoxy-α-D-ribose-1-phosphoric acid	Generator
5-Deoxyribose-1-phosphoric acid	Generator
5-Deoxy-a-D-ribose 1-phosphate	HMDB
5-Deoxy-a-D-ribose 1-phosphoric acid	HMDB
5-Deoxy-alpha-D-ribose 1-phosphoric acid	HMDB
5-Deoxy-α-D-ribose 1-phosphate	HMDB
5-Deoxy-α-D-ribose 1-phosphoric acid	HMDB
5-Deoxyribose-1-phosphate	ChEBI

Molecular Formula

C₅H₁₁O₇P

Average Mass

214.1104

Monoisotopic Mass

214.024239218

IUPAC Name

{[(2R,3R,4S,5R)-3,4-dihydroxy-5-methyloxolan-2-yl]oxy}phosphonic acid

Traditional Name

5-deoxyribose-1-phosphate

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H11O7P/c1-2-3(6)4(7)5(11-2)12-13(8,9)10/h2-7H,1H3,(H2,8,9,10)/t2-,3-,4-,5-/m1/s1

InChI Key

XXQFKXPJJNBLSU-TXICZTDVSA-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
1,2-diol
Oxacycle
Organoheterocyclic compound
Organic oxide
Hydrocarbon derivative
Alcohol
Aliphatic heteromonocyclic compound

Molecular Framework

Aliphatic heteromonocyclic compounds

External Descriptors

5-deoxyribose phosphate (CHEBI:48462 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	37.6 g/L	ALOGPS
logP	-1.5	ALOGPS
logP	-1.4	ChemAxon
logS	-0.76	ALOGPS
pKa (Strongest Acidic)	1.16	ChemAxon
pKa (Strongest Basic)	-3.6	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	2	ChemAxon
Refractivity	39.29 m³·mol⁻¹	ChemAxon
Polarizability	17.12 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 (Non-derivatized) - 70eV, Positive	splash10-0002-9000000000-c8a69fbbc409678cae69	2017-09-20	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0002-9120000000-879348d5449e2ca213cc	2017-10-06	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	Not Available	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-0002-9220000000-5f09dbaee2c5978505dc	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9310000000-114397a9155dbe99d55b	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-9100000000-c4d81d3c665e3a91af96	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03fs-9180000000-dc874a1db4b973ead384	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-801ecd7338d22d460f12	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-28a7bebfe7a8aa82e689	2017-10-06	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014j-9640000000-3ca621ebf36b97197849	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9100000000-8103e0107ce5acf6a5bc	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0006-9000000000-a20a01baf8e1dc7b7d14	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-002b-9000000000-bb9788533e65968dd6ef	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-10-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-10-12	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-24	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
MMDBp0193938	Thymidine phosphorylase	Enzyme	P19971	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0014495	5'-Deoxyadenosine	5-Deoxyribose-1-phosphate	S-methyl-5'-thioadenosine phosphorylase	Phosphorylation	RHEA	34755880
MMDBr0014496	5'-Deoxyadenosine	5-Deoxyribose-1-phosphate	S-methyl-5'-thioadenosine phosphorylase	Phosphorylation	RHEA	34755880
MMDBr0017107	5'-Deoxyribose	5-Deoxyribose-1-phosphate	5-deoxyribose kinase	Phosphorylation	RHEA	34755880
MMDBr0017108	5'-Deoxyribose	5-Deoxyribose-1-phosphate	5-deoxyribose kinase	Phosphorylation	RHEA	34755880
MMDBr0017111	5-Deoxyribose-1-phosphate	5-deoxy-D-ribulose 1-phosphate	5-deoxyribose 1-phosphate isomerase	Isomerization	RHEA	34755880
MMDBr0017112	5-Deoxyribose-1-phosphate	5-deoxy-D-ribulose 1-phosphate	5-deoxyribose 1-phosphate isomerase	Isomerization	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	Proteobacteria	2	Human
Bacteria	Firmicutes	16	Human ; Human feces
Bacteria	Thermotogae	1

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

HMDB0060393

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

C16637

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

24906327

PDB ID

Not Available

ChEBI ID

48462

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Magrane M: UniProt Knowledgebase: a hub of integrated protein data. Database (Oxford). 2011 Mar 29;2011:bar009. doi: 10.1093/database/bar009. Print 2011. [PubMed:21447597 ]

Showing metabocard for 5-Deoxyribose-1-phosphate (MMDBc0052117)

MOL for #<Metabolite:0x00007f5a9849bd40>

3D MOL for #<Metabolite:0x00007f5a9849bd40>

3D SDF for #<Metabolite:0x00007f5a9849bd40>

3D-SDF for #<Metabolite:0x00007f5a9849bd40>

PDB for #<Metabolite:0x00007f5a9849bd40>

3D PDB for #<Metabolite:0x00007f5a9849bd40>

SMILES for #<Metabolite:0x00007f5a9849bd40>

INCHI for #<Metabolite:0x00007f5a9849bd40>

Structure for #<Metabolite:0x00007f5a9849bd40>

3D Structure for #<Metabolite:0x00007f5a9849bd40>