MiMeDB: Showing metabocard for 5'-Deoxyribose (MMDBc0031586)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2021-11-18 01:40:23 UTC

Update Date

2022-08-31 18:21:59 UTC

Metabolite ID

MMDBc0031586

Metabolite Identification

Common Name

5'-Deoxyribose

Description

5'-deoxyribose is a deoxy pentose meaning that it is derived from the sugar ribose by loss of an oxygen atom in the 5' position. The more common form of deoxyribose used in DNA is 2'deoxyribose. 5'-deoxyribose can be formed by the breakdown of 5'deoxyadenosine as catalyzed by 5'-methylthioadenosine/S-adenosylhomocysteine nucleosidase.

Structure

MOL SDF PDB SMILES InChI

45489773
  Mrv0541 07091216292D          

 19 18  0  0  1  0            999 V2000
    3.5220   -1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    2.0930   -0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    4.2365    1.0313    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    5.6655    0.2063    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
    3.5220   -0.2063    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8075    0.2063    0.0000 C   0  0  1  0  0  0  0  0  0  0  0  0
    4.2365    0.2063    0.0000 C   0  0  2  0  0  0  0  0  0  0  0  0
    2.8075    1.0313    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509   -0.2063    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
    3.9650   -0.4620    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075   -0.3053    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6795    0.4620    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.3190    1.0313    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.8075    1.5428    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    2.2960    1.0313    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.9509   -0.7178    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    3.0790   -1.2870    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    1.6500    0.0495    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
    4.6795    1.2870    0.0000 H   0  0  0  0  0  0  0  0  0  0  0  0
  5  1  1  6  0  0  0
  1 17  1  0  0  0  0
  6  2  1  6  0  0  0
  2 18  1  0  0  0  0
  7  3  1  1  0  0  0
  3 19  1  0  0  0  0
  4  9  2  0  0  0  0
  5  6  1  0  0  0  0
  5  7  1  0  0  0  0
  5 10  1  0  0  0  0
  6  8  1  0  0  0  0
  6 11  1  0  0  0  0
  7  9  1  0  0  0  0
  7 12  1  0  0  0  0
  8 13  1  0  0  0  0
  8 14  1  0  0  0  0
  8 15  1  0  0  0  0
  9 16  1  0  0  0  0
M  END
> <DATABASE_ID>
MMDBc0031586

> <DATABASE_NAME>
MIME

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

> <INCHI_IDENTIFIER>
InChI=1S/C5H10O4/c1-3(7)5(9)4(8)2-6/h2-5,7-9H,1H3/t3-,4+,5-/m1/s1

> <INCHI_KEY>
WDRISBUVHBMJEF-MROZADKFSA-N

> <FORMULA>
C5H10O4

> <MOLECULAR_WEIGHT>
134.1305

> <EXACT_MASS>
134.057908808

> <JCHEM_ACCEPTOR_COUNT>
4

> <JCHEM_AVERAGE_POLARIZABILITY>
12.530233860172126

> <JCHEM_BIOAVAILABILITY>
1

> <JCHEM_DONOR_COUNT>
3

> <JCHEM_FORMAL_CHARGE>
0

> <JCHEM_GHOSE_FILTER>
0

> <JCHEM_IUPAC>
(2R,3R,4R)-2,3,4-trihydroxypentanal

> <ALOGPS_LOGP>
-1.74

> <JCHEM_LOGP>
-1.8911156543333332

> <ALOGPS_LOGS>
0.55

> <JCHEM_MDDR_LIKE_RULE>
0

> <JCHEM_NUMBER_OF_RINGS>
0

> <JCHEM_PHYSIOLOGICAL_CHARGE>
0

> <JCHEM_PKA>
12.194042725332771

> <JCHEM_PKA_STRONGEST_ACIDIC>
12.101347856550953

> <JCHEM_PKA_STRONGEST_BASIC>
-3.0539920576398973

> <JCHEM_POLAR_SURFACE_AREA>
77.75999999999999

> <JCHEM_REFRACTIVITY>
29.839399999999998

> <JCHEM_ROTATABLE_BOND_COUNT>
3

> <JCHEM_RULE_OF_FIVE>
1

> <ALOGPS_SOLUBILITY>
4.75e+02 g/l

> <JCHEM_TRADITIONAL_IUPAC>
5'-deoxyribose

> <JCHEM_VEBER_RULE>
0

$$$$

HEADER    PROTEIN                                 09-JUL-12   NONE
TITLE     NULL                                                        
COMPND    MOLECULE: 45489773                                          
SOURCE    NULL                                                        
KEYWDS    NULL                                                        
EXPDTA    NULL                                                        
AUTHOR    Marvin                                                      
REVDAT   1   09-JUL-12         0                                  
HETATM    1  O   UNK     0       6.574  -1.925   0.000  0.00  0.00           O+0
HETATM    2  O   UNK     0       3.907  -0.385   0.000  0.00  0.00           O+0
HETATM    3  O   UNK     0       7.908   1.925   0.000  0.00  0.00           O+0
HETATM    4  O   UNK     0      10.576   0.385   0.000  0.00  0.00           O+0
HETATM    5  C   UNK     0       6.574  -0.385   0.000  0.00  0.00           C+0
HETATM    6  C   UNK     0       5.241   0.385   0.000  0.00  0.00           C+0
HETATM    7  C   UNK     0       7.908   0.385   0.000  0.00  0.00           C+0
HETATM    8  C   UNK     0       5.241   1.925   0.000  0.00  0.00           C+0
HETATM    9  C   UNK     0       9.242  -0.385   0.000  0.00  0.00           C+0
HETATM   10  H   UNK     0       7.401  -0.862   0.000  0.00  0.00           H+0
HETATM   11  H   UNK     0       5.241  -0.570   0.000  0.00  0.00           H+0
HETATM   12  H   UNK     0       8.735   0.862   0.000  0.00  0.00           H+0
HETATM   13  H   UNK     0       6.196   1.925   0.000  0.00  0.00           H+0
HETATM   14  H   UNK     0       5.241   2.880   0.000  0.00  0.00           H+0
HETATM   15  H   UNK     0       4.286   1.925   0.000  0.00  0.00           H+0
HETATM   16  H   UNK     0       9.242  -1.340   0.000  0.00  0.00           H+0
HETATM   17  H   UNK     0       5.747  -2.402   0.000  0.00  0.00           H+0
HETATM   18  H   UNK     0       3.080   0.092   0.000  0.00  0.00           H+0
HETATM   19  H   UNK     0       8.735   2.402   0.000  0.00  0.00           H+0
CONECT    1    5   17                                                       
CONECT    2    6   18                                                       
CONECT    3    7   19                                                       
CONECT    4    9                                                            
CONECT    5    1    6    7   10                                             
CONECT    6    2    5    8   11                                             
CONECT    7    3    5    9   12                                             
CONECT    8    6   13   14   15                                             
CONECT    9    4    7   16                                                  
CONECT   10    5                                                            
CONECT   11    6                                                            
CONECT   12    7                                                            
CONECT   13    8                                                            
CONECT   14    8                                                            
CONECT   15    8                                                            
CONECT   16    9                                                            
CONECT   17    1                                                            
CONECT   18    2                                                            
CONECT   19    3                                                            
MASTER        0    0    0    0    0    0    0    0   19    0   36    0
END

Synonyms

Value	Source
(2R,3R,4R)-2,3,4-Trihydroxypentanal	ChEBI
(2R,3R,4R)-2,3,4-Trihydroxyvaleraldehyde	ChEBI
5-Deoxy-aldehydo-D-ribose	ChEBI
5-Desoxy-D-ribose	ChEBI
D-Ribo-2,3,4-trihydroxyvaleraldehyde	ChEBI
5'-Deoxyribose	ChEBI

Molecular Formula

C₅H₁₀O₄

Average Mass

134.1305

Monoisotopic Mass

134.057908808

IUPAC Name

(2R,3R,4R)-2,3,4-trihydroxypentanal

Traditional Name

5'-deoxyribose

CAS Registry Number

Not Available

SMILES

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

InChI Identifier

InChI=1S/C5H10O4/c1-3(7)5(9)4(8)2-6/h2-5,7-9H,1H3/t3-,4+,5-/m1/s1

InChI Key

WDRISBUVHBMJEF-MROZADKFSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as monosaccharides. Monosaccharides are compounds containing one carbohydrate unit not glycosidically linked to another such unit, and no set of two or more glycosidically linked carbohydrate units. Monosaccharides have the general formula CnH2nOn.

Kingdom

Organic compounds

Super Class

Organic oxygen compounds

Class

Organooxygen compounds

Sub Class

Carbohydrates and carbohydrate conjugates

Direct Parent

Monosaccharides

Alternative Parents

Substituents

Monosaccharide
Beta-hydroxy aldehyde
Alpha-hydroxyaldehyde
Secondary alcohol
Polyol
Organic oxide
Hydrocarbon derivative
Short-chain aldehyde
Carbonyl group
Aldehyde
Alcohol
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

deoxypentose (CHEBI:62012 )

Functional Ontology

Not Available

Physical Properties

State

Expected Solid

Predicted Properties

Property	Value	Source
Water Solubility	475 g/L	ALOGPS
logP	-1.7	ALOGPS
logP	-1.9	ChemAxon
logS	0.55	ALOGPS
pKa (Strongest Acidic)	12.1	ChemAxon
pKa (Strongest Basic)	-3.1	ChemAxon
Physiological Charge	0	ChemAxon
Hydrogen Acceptor Count	4	ChemAxon
Hydrogen Donor Count	3	ChemAxon
Polar Surface Area	77.76 Å²	ChemAxon
Rotatable Bond Count	3	ChemAxon
Refractivity	29.84 m³·mol⁻¹	ChemAxon
Polarizability	12.53 Å³	ChemAxon
Number of Rings	0	ChemAxon
Bioavailability	Yes	ChemAxon
Rule of Five	Yes	ChemAxon
Ghose Filter	No	ChemAxon
Veber's Rule	No	ChemAxon
MDDR-like Rule	No	ChemAxon

Spectra

Not Available

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

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Reaction Type	Data Source	Reference

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/Eubacteria	Proteobacteria	130	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Cattle ; River trout ; Human sputum; Human subgingival plaque; Chicken	Unknown
Bacteria	Proteobacteria	4	Human ; Human feces; Human feces; pleural fluid plaque; bal; Human stool; Pig ; Cattle ; River trout ; Human sputum; Human subgingival plaque; Chicken	Unknown
Bacteria/Eubacteria	Firmicutes	54	Human feces; Human ; Catfish ; Cattle
Bacteria/Eubacteria	Actinobacteria	3	Cattle ; Human
Bacteria/Eubacteria	Thermotogae	1
Bacteria/Eubacteria	Spirochaetes	1	Human
Bacteria	Firmicutes	1	Human feces; Human ; Catfish ; Cattle

Exposure Sources

Other Exposures

Source Type	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

Not Available

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

Not Available

BioCyc ID

CPD0-2167

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

Not Available

PubChem Compound

Not Available

PDB ID

Not Available

ChEBI ID

62012

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Not Available

General References

Bansal P, Morgat A, Axelsen KB, Muthukrishnan V, Coudert E, Aimo L, Hyka-Nouspikel N, Gasteiger E, Kerhornou A, Neto TB, Pozzato M, Blatter MC, Ignatchenko A, Redaschi N, Bridge A: Rhea, the reaction knowledgebase in 2022. Nucleic Acids Res. 2022 Jan 7;50(D1):D693-D700. doi: 10.1093/nar/gkab1016. [PubMed:34755880 ]

Showing metabocard for 5'-Deoxyribose (MMDBc0031586)

MOL for #<Metabolite:0x00007f922b58f9c0>

3D MOL for #<Metabolite:0x00007f922b58f9c0>

3D SDF for #<Metabolite:0x00007f922b58f9c0>

3D-SDF for #<Metabolite:0x00007f922b58f9c0>

PDB for #<Metabolite:0x00007f922b58f9c0>

3D PDB for #<Metabolite:0x00007f922b58f9c0>

SMILES for #<Metabolite:0x00007f922b58f9c0>

INCHI for #<Metabolite:0x00007f922b58f9c0>

Structure for #<Metabolite:0x00007f922b58f9c0>

3D Structure for #<Metabolite:0x00007f922b58f9c0>