NAV

Open Form of 2'-Deoxy-Ribofuranose-5'-Phosphate

Identification

Generic Name
Open Form of 2'-Deoxy-Ribofuranose-5'-Phosphate
DrugBank Accession Number
DB04087
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
3D
Similar Structures
Weight
Average: 216.1263
Monoisotopic: 216.039889282
Chemical Formula
C5H13O7P
Synonyms
Not Available
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Pharmacology

Indication

Not Available

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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
UDeoxyribose-phosphate aldolaseNot AvailableEscherichia coli (strain K12)
UDeoxyribose-phosphate aldolaseNot AvailableThermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Absorption

Not Available

Volume of distribution

Not Available

Protein binding

Not Available

Metabolism
Not Available
Route of elimination

Not Available

Half-life

Not Available

Clearance

Not Available

Adverse Effects
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Toxicity

Not Available

Pathways
Not Available
Pharmacogenomic Effects/ADRs
Not Available

Interactions

Drug Interactions
This information should not be interpreted without the help of a healthcare provider. If you believe you are experiencing an interaction, contact a healthcare provider immediately. The absence of an interaction does not necessarily mean no interactions exist.
Not Available
Food Interactions
Not Available

Categories

Drug Categories
Not Available
Chemical TaxonomyProvided by Classyfire
Description
This compound belongs to the class of organic compounds known as monoalkyl phosphates. These are organic compounds containing a phosphate group that is linked to exactly one alkyl chain.
Kingdom
Organic compounds
Super Class
Organic acids and derivatives
Class
Organic phosphoric acids and derivatives
Sub Class
Phosphate esters
Direct Parent
Monoalkyl phosphates
Alternative Parents
Secondary alcohols / Polyols / Primary alcohols / Organic oxides / Hydrocarbon derivatives
Substituents
Alcohol / Aliphatic acyclic compound / Hydrocarbon derivative / Monoalkyl phosphate / Organic oxide / Organic oxygen compound / Organooxygen compound / Polyol / Primary alcohol / Secondary alcohol
Molecular Framework
Aliphatic acyclic compounds
External Descriptors
Not Available
Affected organisms
Not Available

Chemical Identifiers

UNII
Not Available
CAS number
Not Available
InChI Key
YCHBTVQJICBXEI-CRCLSJGQSA-N
InChI
InChI=1S/C5H13O7P/c6-2-1-4(7)5(8)3-12-13(9,10)11/h4-8H,1-3H2,(H2,9,10,11)/t4-,5+/m0/s1
IUPAC Name
{[(2R,3S)-2,3,5-trihydroxypentyl]oxy}phosphonic acid
SMILES
[H][C@](O)(CCO)[C@]([H])(O)COP(O)(O)=O

References

General References
Not Available
PubChem Compound
5288577
PubChem Substance
46508398
ChemSpider
4450713
PDBe Ligand
HPD
PDB Entries
1jcj / 1jcl / 1l1t / 1l2c / 1l2d / 1rrs / 1ub3 / 1vrl

Clinical Trials

Clinical Trials
PhaseStatusPurposeConditionsCount

Pharmacoeconomics

Manufacturers
Not Available
Packagers
Not Available
Dosage Forms
Not Available
Prices
Not Available
Patents
Not Available

Properties

State
Solid
Experimental Properties
Not Available
Predicted Properties
PropertyValueSource
Water Solubility33.0 mg/mLALOGPS
logP-1.9ALOGPS
logP-2.5Chemaxon
logS-0.82ALOGPS
pKa (Strongest Acidic)1.5Chemaxon
pKa (Strongest Basic)-2.4Chemaxon
Physiological Charge-2Chemaxon
Hydrogen Acceptor Count6Chemaxon
Hydrogen Donor Count5Chemaxon
Polar Surface Area127.45 Å2Chemaxon
Rotatable Bond Count6Chemaxon
Refractivity42.22 m3·mol-1Chemaxon
Polarizability18.08 Å3Chemaxon
Number of Rings0Chemaxon
Bioavailability1Chemaxon
Rule of FiveYesChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleNoChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption-0.9386
Blood Brain Barrier+0.6608
Caco-2 permeable-0.6995
P-glycoprotein substrateNon-substrate0.6164
P-glycoprotein inhibitor INon-inhibitor0.8271
P-glycoprotein inhibitor IINon-inhibitor0.8988
Renal organic cation transporterNon-inhibitor0.915
CYP450 2C9 substrateNon-substrate0.8351
CYP450 2D6 substrateNon-substrate0.8239
CYP450 3A4 substrateNon-substrate0.6331
CYP450 1A2 substrateNon-inhibitor0.8603
CYP450 2C9 inhibitorNon-inhibitor0.869
CYP450 2D6 inhibitorNon-inhibitor0.9169
CYP450 2C19 inhibitorNon-inhibitor0.8429
CYP450 3A4 inhibitorNon-inhibitor0.9628
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9659
Ames testNon AMES toxic0.8552
CarcinogenicityNon-carcinogens0.7556
BiodegradationNot ready biodegradable0.519
Rat acute toxicity1.8322 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.7606
hERG inhibition (predictor II)Non-inhibitor0.7402
ADMET data is predicted using admetSAR, a free tool for evaluating chemical ADMET properties. (23092397)

Spectra

Mass Spec (NIST)
Not Available
Spectra
SpectrumSpectrum TypeSplash Key
Predicted GC-MS Spectrum - GC-MSPredicted GC-MSsplash10-0002-9400000000-d8da717d7285a6fbef47
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-0002-9210000000-8ca17bc93a28b6076376
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-0002-9000000000-a5dddf44e01ccc8c9888
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-004j-9000000000-d58367be3fdfc9f0cb66
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-0002-9200000000-9fbeee91ebc3ef63a2be
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9000000000-4f7c75bb721ac148a7fa
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-0002-9000000000-59d9e6f1326f8d2600dd
Predicted 1H NMR Spectrum1D NMRNot Applicable
Predicted 13C NMR Spectrum1D NMRNot Applicable
Chromatographic Properties
Collision Cross Sections (CCS)
AdductCCS Value (Å2)Source typeSource
[M-H]-132.26744
predicted
DeepCCS 1.0 (2019)
[M+H]+134.66597
predicted
DeepCCS 1.0 (2019)
[M+Na]+140.57552
predicted
DeepCCS 1.0 (2019)

Targets

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Details1. Deoxyribose-phosphate aldolase
Kind
Protein
Organism
Escherichia coli (strain K12)
Pharmacological action
Unknown
General Function
Lyase activity
Specific Function
Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.
Gene Name
deoC
Uniprot ID
P0A6L0
Uniprot Name
Deoxyribose-phosphate aldolase
Molecular Weight
27733.44 Da
References
  1. Overington JP, Al-Lazikani B, Hopkins AL: How many drug targets are there? Nat Rev Drug Discov. 2006 Dec;5(12):993-6. [Article]
  2. Imming P, Sinning C, Meyer A: Drugs, their targets and the nature and number of drug targets. Nat Rev Drug Discov. 2006 Oct;5(10):821-34. [Article]
Details2. Deoxyribose-phosphate aldolase
Kind
Protein
Organism
Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)
Pharmacological action
Unknown
General Function
Deoxyribose-phosphate aldolase activity
Specific Function
Catalyzes a reversible aldol reaction between acetaldehyde and D-glyceraldehyde 3-phosphate to generate 2-deoxy-D-ribose 5-phosphate.
Gene Name
deoC
Uniprot ID
Q5SJ28
Uniprot Name
Deoxyribose-phosphate aldolase
Molecular Weight
23306.525 Da
References
  1. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The Protein Data Bank. Nucleic Acids Res. 2000 Jan 1;28(1):235-42. [Article]

Drug created at June 13, 2005 13:24 / Updated at June 12, 2020 16:52