Dpb-T

Identification

Generic Name
Dpb-T
DrugBank Accession Number
DB02217
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
Weight
Average: 410.3151
Monoisotopic: 410.087902106
Chemical Formula
C17H19N2O8P
Synonyms
Not Available

Pharmacology

Indication

Not Available

Reduce drug development failure rates
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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
U5'(3')-deoxyribonucleotidase, mitochondrialNot AvailableHumans
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 pyrimidones. These are compounds that contain a pyrimidine ring, which bears a ketone. Pyrimidine is a 6-membered ring consisting of four carbon atoms and two nitrogen centers at the 1- and 3- ring positions.
Kingdom
Organic compounds
Super Class
Organoheterocyclic compounds
Class
Diazines
Sub Class
Pyrimidines and pyrimidine derivatives
Direct Parent
Pyrimidones
Alternative Parents
1,3-dioxanes / Benzene and substituted derivatives / Hydropyrimidines / Vinylogous amides / Tetrahydrofurans / Heteroaromatic compounds / Organic phosphonic acids / Ureas / Lactams / Oxacyclic compounds
show 7 more
Substituents
Aromatic heteropolycyclic compound / Azacycle / Benzenoid / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine / Lactam / Meta-dioxane / Monocyclic benzene moiety / Organic nitrogen compound
show 13 more
Molecular Framework
Aromatic heteropolycyclic compounds
External Descriptors
pyrimidine 2'-deoxyribonucleoside (CHEBI:42198)
Affected organisms
Not Available

Chemical Identifiers

UNII
Not Available
CAS number
Not Available
InChI Key
WTZFKHNHHRPQOU-WSMBLCCSSA-N
InChI
InChI=1S/C17H19N2O8P/c1-10-8-19(16(21)18-15(10)20)14-7-12-13(26-14)9-25-17(27-12,28(22,23)24)11-5-3-2-4-6-11/h2-6,8,12-14H,7,9H2,1H3,(H,18,20,21)(H2,22,23,24)/t12-,13-,14-,17-/m0/s1
IUPAC Name
[(2S,4aS,6S,7aS)-6-(5-methyl-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-yl)-2-phenyl-hexahydrofuro[3,2-d][1,3]dioxin-2-yl]phosphonic acid
SMILES
[H][C@]1(C[C@]2([H])O[C@@](OC[C@]2([H])O1)(C1=CC=CC=C1)P(O)(O)=O)N1C=C(C)C(=O)NC1=O

References

General References
Not Available
PubChem Compound
5288101
PubChem Substance
46508258
ChemSpider
4450335
ZINC
ZINC000012501733
PDBe Ligand
DPB
PDB Entries
1q91

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 Solubility4.43 mg/mLALOGPS
logP-0.25ALOGPS
logP0.97Chemaxon
logS-2ALOGPS
pKa (Strongest Acidic)0.65Chemaxon
pKa (Strongest Basic)-3.9Chemaxon
Physiological Charge-2Chemaxon
Hydrogen Acceptor Count8Chemaxon
Hydrogen Donor Count3Chemaxon
Polar Surface Area134.63 Å2Chemaxon
Rotatable Bond Count3Chemaxon
Refractivity93.93 m3·mol-1Chemaxon
Polarizability36.12 Å3Chemaxon
Number of Rings4Chemaxon
Bioavailability1Chemaxon
Rule of FiveYesChemaxon
Ghose FilterYesChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleNoChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption-0.5728
Blood Brain Barrier+0.6135
Caco-2 permeable-0.7273
P-glycoprotein substrateNon-substrate0.6436
P-glycoprotein inhibitor INon-inhibitor0.8561
P-glycoprotein inhibitor IINon-inhibitor0.987
Renal organic cation transporterNon-inhibitor0.8862
CYP450 2C9 substrateNon-substrate0.5692
CYP450 2D6 substrateNon-substrate0.8504
CYP450 3A4 substrateSubstrate0.5842
CYP450 1A2 substrateNon-inhibitor0.8629
CYP450 2C9 inhibitorNon-inhibitor0.8151
CYP450 2D6 inhibitorNon-inhibitor0.9109
CYP450 2C19 inhibitorNon-inhibitor0.7999
CYP450 3A4 inhibitorNon-inhibitor0.771
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.8643
Ames testNon AMES toxic0.6151
CarcinogenicityNon-carcinogens0.8124
BiodegradationNot ready biodegradable0.7116
Rat acute toxicity2.5078 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.9604
hERG inhibition (predictor II)Non-inhibitor0.7877
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 MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-01p9-0090700000-655ae1bbc676ae5f2990
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-0gy9-0095300000-cf2342c82495b119fee4
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-056r-3009600000-8b234a1c8a80b779720c
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-0zi0-6597100000-fd8c197fdf8be8e33db5
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-004i-9001000000-dbd9e7d451092d62730b
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-01t9-9324000000-020c9ac51bd1e18924e6
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]-183.46315
predicted
DeepCCS 1.0 (2019)
[M+H]+185.56776
predicted
DeepCCS 1.0 (2019)
[M+Na]+191.48106
predicted
DeepCCS 1.0 (2019)

Targets

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Kind
Protein
Organism
Humans
Pharmacological action
Unknown
General Function
Nucleotide binding
Specific Function
Dephosphorylates specifically the 5' and 2'(3')-phosphates of uracil and thymine deoxyribonucleotides, and so protects mitochondrial DNA replication from excess dTTP. Has only marginal activity tow...
Gene Name
NT5M
Uniprot ID
Q9NPB1
Uniprot Name
5'(3')-deoxyribonucleotidase, mitochondrial
Molecular Weight
25861.505 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]
  3. 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