4-Amino-5-Hydroxymethyl-2-Methylpyrimidine

Identification

Generic Name
4-Amino-5-Hydroxymethyl-2-Methylpyrimidine
DrugBank Accession Number
DB02022
Background

Not Available

Type
Small Molecule
Groups
Experimental
Structure
Weight
Average: 139.1552
Monoisotopic: 139.074561925
Chemical Formula
C6H9N3O
Synonyms
Not Available

Pharmacology

Indication

Not Available

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Pharmacodynamics

Not Available

Mechanism of action
TargetActionsOrganism
UThiaminase-2Not AvailableBacillus subtilis (strain 168)
UHydroxymethylpyrimidine/phosphomethylpyrimidine kinaseNot AvailableSalmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
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 hydropyrimidines. These are compounds containing a hydrogenated pyrimidine ring (i.e. containing less than the maximum number of double bonds.).
Kingdom
Organic compounds
Super Class
Organoheterocyclic compounds
Class
Diazines
Sub Class
Pyrimidines and pyrimidine derivatives
Direct Parent
Hydropyrimidines
Alternative Parents
Imidolactams / Heteroaromatic compounds / Azacyclic compounds / Primary alcohols / Organopnictogen compounds / Organonitrogen compounds / Hydrocarbon derivatives / Aromatic alcohols
Substituents
Alcohol / Aromatic alcohol / Aromatic heteromonocyclic compound / Azacycle / Heteroaromatic compound / Hydrocarbon derivative / Hydropyrimidine / Imidolactam / Organic nitrogen compound / Organic oxygen compound
Molecular Framework
Aromatic heteromonocyclic compounds
External Descriptors
aminopyrimidine, aromatic primary alcohol (CHEBI:16892) / a small molecule (HMP)
Affected organisms
Not Available

Chemical Identifiers

UNII
G62V17J09J
CAS number
73-67-6
InChI Key
VUTBELPREDJDDH-UHFFFAOYSA-N
InChI
InChI=1S/C6H9N3O/c1-4-8-2-5(3-10)6(7)9-4/h2,10H,3H2,1H3,(H2,7,8,9)
IUPAC Name
(4-amino-2-methylpyrimidin-5-yl)methanol
SMILES
CC1=NC=C(CO)C(N)=N1

References

General References
Not Available
KEGG Compound
C01279
PubChem Compound
777
PubChem Substance
46508420
ChemSpider
756
ChEBI
16892
ZINC
ZINC000000895559
PDBe Ligand
HMH
PDB Entries
1jxi / 1to9 / 1yak / 2f2g / 2gm8 / 2q4x / 3epm / 7r8y

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
PropertyValueSource
melting point (°C)198 °CPhysProp
Predicted Properties
PropertyValueSource
Water Solubility12.0 mg/mLALOGPS
logP-0.26ALOGPS
logP-0.36Chemaxon
logS-1.1ALOGPS
pKa (Strongest Acidic)14.41Chemaxon
pKa (Strongest Basic)6.17Chemaxon
Physiological Charge1Chemaxon
Hydrogen Acceptor Count4Chemaxon
Hydrogen Donor Count2Chemaxon
Polar Surface Area72.03 Å2Chemaxon
Rotatable Bond Count1Chemaxon
Refractivity39.18 m3·mol-1Chemaxon
Polarizability14.2 Å3Chemaxon
Number of Rings1Chemaxon
Bioavailability1Chemaxon
Rule of FiveYesChemaxon
Ghose FilterNoChemaxon
Veber's RuleNoChemaxon
MDDR-like RuleNoChemaxon
Predicted ADMET Features
PropertyValueProbability
Human Intestinal Absorption+0.9357
Blood Brain Barrier+0.9337
Caco-2 permeable-0.5088
P-glycoprotein substrateNon-substrate0.7661
P-glycoprotein inhibitor INon-inhibitor0.9727
P-glycoprotein inhibitor IINon-inhibitor0.9668
Renal organic cation transporterNon-inhibitor0.8806
CYP450 2C9 substrateNon-substrate0.7949
CYP450 2D6 substrateNon-substrate0.8522
CYP450 3A4 substrateNon-substrate0.8292
CYP450 1A2 substrateNon-inhibitor0.534
CYP450 2C9 inhibitorNon-inhibitor0.9712
CYP450 2D6 inhibitorNon-inhibitor0.886
CYP450 2C19 inhibitorNon-inhibitor0.8974
CYP450 3A4 inhibitorNon-inhibitor0.9189
CYP450 inhibitory promiscuityLow CYP Inhibitory Promiscuity0.9559
Ames testAMES toxic0.6092
CarcinogenicityNon-carcinogens0.8749
BiodegradationNot ready biodegradable0.8727
Rat acute toxicity2.2154 LD50, mol/kg Not applicable
hERG inhibition (predictor I)Weak inhibitor0.961
hERG inhibition (predictor II)Non-inhibitor0.9113
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-MSsplash10-0abi-1900000000-e3106b1f3a699dcbb5cf
Predicted MS/MS Spectrum - 10V, Positive (Annotated)Predicted LC-MS/MSsplash10-00dl-1900000000-363fb8f526202ba41c0c
Predicted MS/MS Spectrum - 10V, Negative (Annotated)Predicted LC-MS/MSsplash10-000i-3900000000-58300369bb6e80f49d8c
Predicted MS/MS Spectrum - 20V, Positive (Annotated)Predicted LC-MS/MSsplash10-0089-9600000000-5029f83c81ecbdc0ab16
Predicted MS/MS Spectrum - 20V, Negative (Annotated)Predicted LC-MS/MSsplash10-0006-9300000000-d722040ded096814f50b
Predicted MS/MS Spectrum - 40V, Positive (Annotated)Predicted LC-MS/MSsplash10-0fai-9000000000-2ac0b21b494f58c9fa64
Predicted MS/MS Spectrum - 40V, Negative (Annotated)Predicted LC-MS/MSsplash10-00kf-9000000000-48177106aaff9954e705
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]-129.1212277
predicted
DarkChem Lite v0.1.0
[M-H]-129.2280277
predicted
DarkChem Lite v0.1.0
[M-H]-130.2962
predicted
DeepCCS 1.0 (2019)
[M+H]+128.8680277
predicted
DarkChem Lite v0.1.0
[M+H]+128.8406277
predicted
DarkChem Lite v0.1.0
[M+H]+134.0849
predicted
DeepCCS 1.0 (2019)
[M+Na]+129.3102277
predicted
DarkChem Lite v0.1.0
[M+Na]+129.2314277
predicted
DarkChem Lite v0.1.0
[M+Na]+143.10127
predicted
DeepCCS 1.0 (2019)

Targets

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Kind
Protein
Organism
Bacillus subtilis (strain 168)
Pharmacological action
Unknown
General Function
Thiaminase activity
Specific Function
Catalyzes an amino-pyrimidine hydrolysis reaction at the C5' of the pyrimidine moiety of thiamine compounds, a reaction that is part of a thiamine salvage pathway. Thus, catalyzes the conversion of...
Gene Name
tenA
Uniprot ID
P25052
Uniprot Name
Aminopyrimidine aminohydrolase
Molecular Weight
27416.405 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]
Kind
Protein
Organism
Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)
Pharmacological action
Unknown
General Function
Phosphomethylpyrimidine kinase activity
Specific Function
Catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate (HMP-P) to HMP-PP, and of HMP to HMP-P.
Gene Name
thiD
Uniprot ID
P55882
Uniprot Name
Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase
Molecular Weight
28543.305 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]

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