MiMeDB: Showing metabocard for Deoxyribose 5-phosphate (MMDBc0029533)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-17 23:31:18 UTC

Update Date

2022-08-31 13:42:32 UTC

Metabolite ID

MMDBc0029533

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>
MMDBc0029533

> <DATABASE_NAME>
MIME

> <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

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

Molecular Formula

C₅H₁₁O₇P

Average Mass

214.1104

Monoisotopic Mass

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 )

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted 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

Spectra

Spectrum Type	Description	Splash Key	Deposition Date	View
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (Non-derivatized) - 70eV, Positive	splash10-0002-9600000000-bdc9f54852e365293f11	2016-09-22	View Spectrum
Predicted GC-MS	Predicted GC-MS Spectrum - GC-MS (2 TMS) - 70eV, Positive	splash10-006x-9185000000-bfea5991ff0a9475e0b9	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	splash10-014i-3970000000-30d79004fa4e6fa5906d	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00kb-7910000000-3de23781c803b806a189	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-052b-9100000000-25bca847c2e30ed7e327	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-03fr-8490000000-6979c10cf3fafe02069d	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Negative	splash10-004i-9100000000-43a8b73209f01319d3c2	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Negative	splash10-004i-9000000000-16fc473b541d2a247daf	2016-09-12	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Positive	splash10-014j-8910000000-7c465e8be120df2e083a	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 20V, Positive	splash10-00r2-9200000000-4f0c0c2bf45b1986dd6a	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 40V, Positive	splash10-0002-9100000000-a91ae5a4e7423371ee52	2021-09-23	View Spectrum
Predicted LC-MS/MS	Predicted LC-MS/MS Spectrum - 10V, Negative	splash10-01r2-9030000000-5eb77e97817ae8e3e50f	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, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 100 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 200 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 300 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 400 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 500 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 600 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 700 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 800 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 900 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹³C NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-16	View Spectrum
1D NMR	¹H NMR Spectrum (1D, 1000 MHz, D₂O, predicted)		2021-09-16	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
MMDBp0192563	Putative deoxyribose-phosphate aldolase	Enzyme	Q9Y315	Homo sapiens
MMDBp0192694	Ribokinase	Enzyme	Q9H477	Homo sapiens
MMDBp0193931	Phosphoglucomutase-2	Unknown	Q96G03	Homo sapiens

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference
MMDBr0000828	Deoxyribose 5-phosphate	Acetaldehyde	Not Available	Deoxyribose-Phosphate Aldolase	VMH	30371894
MMDBr0007611	Deoxyribose 1-phosphate	Deoxyribose 5-phosphate	Not Available	2-Deoxy-D-Ribose 1-Phosphate 1, 5-Phosphomutase Ec:5.4.2.7	VMH	30371894
MMDBr0007754	Adenosine triphosphate	Deoxyribose 5-phosphate	Not Available	Deoxyribokinase	VMH	30371894
MMDBr0007756	Deoxyribose 5-phosphate	Acetaldehyde	Not Available	2-Deoxy-D-ribose-5-phosphate acetaldehyde-lyase	VMH	30371894
MMDBr0019320	Deoxyribose 1-phosphate	Deoxyribose 5-phosphate	Phosphopentomutase	Transfers of a phosphate group; Isomerization; Intramolecular transfer of functional group	PathBank	31602464
MMDBr0019321	Deoxyribose 5-phosphate	Acetaldehyde	Deoxyribose-phosphate aldolase	Aldol addition (or reverse)	PathBank	31602464
MMDBr0024435	Deoxyribose 5-phosphate	Acetaldehyde	Deoxyribose-phosphate aldolase	Aldol addition (or reverse)	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
MMDBr0025428	Water	Thymine	Pyrimidine/purine nucleotide 5'-monophosphate nucleosidase	Hydrolysis of a nucleotide	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	Microbial Links
Bacteria	Proteobacteria	137	Human ; Human feces; Human sputum; 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	377	Human feces; Human pleural fluid plaque; Pig ; Human sputum; Human ; Human subgingival plaque; Human saliva; Human urine; Human mucosa; Human supragingival plaque; Cattle	Metabolic reconstruction
Bacteria	Actinobacteria	108	Human feces; Human sputum; Human bronchial brush; Human nasopharyngeal swab; Human pleural fluid plaque; Human dental plaque; Human ; Human supragingival plaque; Human mucosa; Human subgingival plaque; Human saliva	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	126	Human feces; Human appendix biopsy; Human ; Human stool; Human saliva; Human gastric fluid; Human urine; Human supragingival plaque; Human subgingival plaque	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	9	Human feces; Human	Metabolic reconstruction
Archaea	Euryarchaeota	4		Metabolic reconstruction
Bacteria	Candidatus melainabacteria	1	Human feces	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

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
Human Feces	Detected but not Quantified									HMDB

External Links

HMDB ID

HMDB0001031

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

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for Deoxyribose 5-phosphate (MMDBc0029533)

MOL for #<Metabolite:0x00007f5abc304c10>

3D MOL for #<Metabolite:0x00007f5abc304c10>

3D SDF for #<Metabolite:0x00007f5abc304c10>

3D-SDF for #<Metabolite:0x00007f5abc304c10>

PDB for #<Metabolite:0x00007f5abc304c10>

3D PDB for #<Metabolite:0x00007f5abc304c10>

SMILES for #<Metabolite:0x00007f5abc304c10>

INCHI for #<Metabolite:0x00007f5abc304c10>

Structure for #<Metabolite:0x00007f5abc304c10>

3D Structure for #<Metabolite:0x00007f5abc304c10>