ChemFOnt: Showing chemical card for 2-Deoxyribonic acid (CFc000000266)

Record Information

Version

1.0

Creation Date

2022-08-28 10:25:12 UTC

Update Date

2022-09-13 18:44:37 UTC

Chemfont ID

CFc000000266

Molecule Identification

Common Name

2-Deoxyribonic acid

Definition

2-Deoxyribonic acid is the acid form of deoxyribonate (interconvertible with 2-Deoxyribonolactone), produced as part of bistranded lesions by DNA damaging agents, including the antitumor agents bleomycin and the neocarzinostatin chromophore (PMID 2523732 ). This lesion is also produced by ionizing radiation, organometallic oxidants, and is a metastable intermediate in DNA damage mediated by copper phenanthroline nucleases, and is also formed under anaerobic conditions in the presence of the radiosensitizing agent tirapazamine. (PMID 12600212 ), and it has been found in normal human biofluids (PMID 2925825 , 3829393 , 6725493 , 7228943 ).

Structure

MOL SDF PDB SMILES InChI

Synonyms

Value	Source
2-Deoxyribonate	Generator
2-Deoxy-D-ribonate	HMDB
2-Deoxy-D-ribonic acid	HMDB

Chemical Formula

C₅H₁₀O₅

Average Molecular Weight

150.1299

Monoisotopic Molecular Weight

150.05282343

IUPAC Name

(3S,4R)-3,4,5-trihydroxypentanoic acid

Traditional Name

(3S,4R)-3,4,5-trihydroxypentanoic acid

CAS Registry Number

29625-75-0

SMILES

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

InChI Identifier

InChI=1S/C5H10O5/c6-2-4(8)3(7)1-5(9)10/h3-4,6-8H,1-2H2,(H,9,10)/t3-,4+/m0/s1

InChI Key

VBUWJOHKCBQXNU-IUYQGCFVSA-N

Chemical Taxonomy

Description

Belongs to the class of organic compounds known as beta hydroxy acids and derivatives. Beta hydroxy acids and derivatives are compounds containing a carboxylic acid substituted with a hydroxyl group on the C3 carbon atom.

Kingdom

Organic compounds

Super Class

Organic acids and derivatives

Class

Hydroxy acids and derivatives

Sub Class

Beta hydroxy acids and derivatives

Direct Parent

Beta hydroxy acids and derivatives

Alternative Parents

Substituents

Beta-hydroxy acid
Short-chain hydroxy acid
Fatty acid
Secondary alcohol
Carboxylic acid derivative
Carboxylic acid
Monocarboxylic acid or derivatives
Polyol
Organooxygen compound
Organic oxygen compound
Alcohol
Carbonyl group
Primary alcohol
Organic oxide
Hydrocarbon derivative
Aliphatic acyclic compound

Molecular Framework

Aliphatic acyclic compounds

External Descriptors

pentonic acid (CHEBI:86350 )

Functional Ontology

Not Available

Urine (PMID: 28157703)

Source

Endogenous

Endogenous (HMDB: HMDB0000366)

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

Not Available

Role

Not Available

Physical Properties

Predicted Properties

Property	Value	Source
Water Solubility	511 g/L	ALOGPS
logP	-2	ALOGPS
logP	-2.1	ChemAxon
logS	0.53	ALOGPS
pKa (Strongest Acidic)	4.03	ChemAxon
pKa (Strongest Basic)	-3	ChemAxon
Physiological Charge	-1	ChemAxon
Hydrogen Acceptor Count	5	ChemAxon
Hydrogen Donor Count	4	ChemAxon
Polar Surface Area	97.99 Å²	ChemAxon
Rotatable Bond Count	4	ChemAxon
Refractivity	30.97 m³·mol⁻¹	ChemAxon
Polarizability	13.51 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

External Links

HMDB ID

HMDB0000366

DrugBank ID

Not Available

Phenol Explorer Compound ID

Not Available

FooDB ID

FDB021985

KNApSAcK ID

Not Available

Chemspider ID

9703151

KEGG Compound ID

Not Available

BioCyc ID

Not Available

BiGG ID

Not Available

Wikipedia Link

Not Available

METLIN ID

5355

PubChem Compound

11528367

PDB ID

Not Available

ChEBI ID

86350

Food Biomarker Ontology

Not Available

References

Synthesis Reference

Yang, Byung Yun; Montgomery, Rex. Alkaline degradation of fructofuranosides. Carbohydrate Research (1996), 280(1), 47-57.

Showing chemical card for 2-Deoxyribonic acid (CFc000000266)

MOL for CFc000000266 (2-Deoxyribonic acid)

3D MOL for CFc000000266 (2-Deoxyribonic acid)

3D SDF for CFc000000266 (2-Deoxyribonic acid)

3D-SDF for CFc000000266 (2-Deoxyribonic acid)

PDB for CFc000000266 (2-Deoxyribonic acid)

3D PDB for CFc000000266 (2-Deoxyribonic acid)

SMILES for CFc000000266 (2-Deoxyribonic acid)

INCHI for CFc000000266 (2-Deoxyribonic acid)

Structure for CFc000000266 (2-Deoxyribonic acid)

3D Structure for CFc000000266 (2-Deoxyribonic acid)