MiMeDB: Showing metabocard for Deoxyribose 1-phosphate (MMDBc0029628)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:35:15 UTC

Update Date

2024-04-30 19:39:41 UTC

Metabolite ID

MMDBc0029628

Metabolite Identification

Common Name

Deoxyribose 1-phosphate

Description

Deoxyribose 1-phosphate is an intermediate in the metabolism of Pyrimidine. It is a substrate for Purine nucleoside phosphorylase and Thymidine phosphorylase.

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>
MMDBc0029628

> <DATABASE_NAME>
MIME

> <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

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

Molecular Formula

C₅H₁₁O₇P

Average Mass

214.1104

Monoisotopic Mass

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 )

Functional Ontology

Not Available

Physical Properties

State

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	17.21 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9100000000-0b83a26b67c41b7ca8c9	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-0002-9120000000-ed5a733798dcf4d7c439	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	splash10-00kb-9430000000-ef11f7c98a651dbe59d7	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9400000000-5e3754bb21aff6c3ce06	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-9300000000-615ca1fa907e42aa9c9d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03fs-9260000000-5a7b6b1faaba56e1c97d	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-5f0b0b093f8d726f7076	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-b1cd1b026728c07d36bb	2015-09-15	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014i-3690000000-41b666017994305912b8	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-0002-9200000000-99440f284bdeb59e2f04	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052b-9000000000-f613851350f97d5430bc	2021-09-22	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03fr-9080000000-e66a31856a5562cb0b9d	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-25	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-a5e502a2627af2048a1f	2021-09-25	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, H₂O, predicted)		2022-08-18	View Spectrum

Biological Properties

Cellular Locations

Cytoplasm

Biospecimen Locations

Feces

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
MMDBp0192694	Ribokinase	Enzyme	Q9H477	Homo sapiens
MMDBp0193931	Phosphoglucomutase-2	Unknown	Q96G03	Homo sapiens
MMDBp0193933	Purine nucleoside phosphorylase	Enzyme	P00491	Homo sapiens
MMDBp0193938	Thymidine phosphorylase	Enzyme	P19971	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0000040	Deoxyribose 1-phosphate	Deoxyribose	Not Available	VMH	9693094
MMDBr0002257	Thymidine	Deoxyribose 1-phosphate	Not Available	VMH; KEGG	30371894
MMDBr0007324	Deoxyuridine	Deoxyribose 1-phosphate	Not Available	VMH; KEGG	30371894
MMDBr0007554	Deoxyadenosine	Deoxyribose 1-phosphate	Not Available	VMH; KEGG	30371894
MMDBr0007556	Deoxyguanosine	Deoxyribose 1-phosphate	Not Available	VMH; KEGG	30371894
MMDBr0007558	Deoxyinosine	Deoxyribose 1-phosphate	Not Available	VMH; KEGG	30371894
MMDBr0007611	Deoxyribose 1-phosphate	Deoxyribose 5-phosphate	Not Available	VMH	30371894

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	Microbial Links
Bacteria	Proteobacteria	140	Human feces; Human sputum; Human ; Human unknown; Pig ; Human pleural fluid plaque; Human dental plaque; Human nasal swab; Human stool; Human feces; pleural fluid plaque; bal	Unknown; Metabolic reconstruction
Bacteria	Firmicutes	349	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle ; Human stool	Metabolic reconstruction
Bacteria	Actinobacteria	74	Human feces; Human pleural fluid plaque; Human dental plaque; Human sputum; Human ; Human nasopharyngeal swab; Human mucosa; Human supragingival plaque; Human subgingival plaque	Metabolic reconstruction
Bacteria	Bacteroidetes	123	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Bacteria	Fusobacteria	20	Human feces; Human	Metabolic reconstruction
Bacteria	Candidatus melainabacteria	1	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	1		Metabolic reconstruction
Bacteria	Tenericutes	4	Human feces	Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1	Human feces; Human saliva	Unknown

Exposure Sources

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0001351

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

References

Synthesis Reference

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. doi: 10.1016/s0891-5849(98)00181-6. [PubMed:9890648 ]

Showing metabocard for Deoxyribose 1-phosphate (MMDBc0029628)

MOL for #<Metabolite:0x00007fdb4d02ce18>

3D MOL for #<Metabolite:0x00007fdb4d02ce18>

3D SDF for #<Metabolite:0x00007fdb4d02ce18>

3D-SDF for #<Metabolite:0x00007fdb4d02ce18>

PDB for #<Metabolite:0x00007fdb4d02ce18>

3D PDB for #<Metabolite:0x00007fdb4d02ce18>

SMILES for #<Metabolite:0x00007fdb4d02ce18>

INCHI for #<Metabolite:0x00007fdb4d02ce18>

Structure for #<Metabolite:0x00007fdb4d02ce18>

3D Structure for #<Metabolite:0x00007fdb4d02ce18>