Structure of PDB 3kr1 Chain A Binding Site BS02

Receptor Information
>3kr1 Chain A (length=257) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
ASAYQRFEPRAYLRNNYAPPRGDLCNPNGVGPWKLRCLAQTFATGEVSGR
TLIDIGSGPTVYQLLSACSHFEDITMTDFLEVNRQELGRWLQEEPGAFNW
SMYSQHACLIEGKGECWQDKERQLRARVKRVLPIDVHQPQPLGAGSPAPL
PADALVSAFCLEAVSPDLASFQRALDHITTLLRPGGHLLLIGALEESWYL
AGEARLTVVPVSEEEVREALVRSGYKVRDLRTYIMPAHLQTGVDDVKGVF
FAWAQKV
Ligand information
Ligand IDVGD
InChIInChI=1S/C7H6ClN3/c8-4-1-2-5-6(3-4)11-7(9)10-5/h1-3H,(H3,9,10,11)
InChIKeyPDOCNPCPPLPXRV-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Clc2cc1c(nc(n1)N)cc2
CACTVS 3.341Nc1[nH]c2cc(Cl)ccc2n1
OpenEye OEToolkits 1.5.0c1cc2c(cc1Cl)[nH]c(n2)N
FormulaC7 H6 Cl N3
Name6-chloro-1H-benzimidazol-2-amine
ChEMBLCHEMBL269158
DrugBank
ZINCZINC000005425419
PDB chain3kr1 Chain A Residue 290 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kr1 Fragment-based screening by X-ray crystallography, MS and isothermal titration calorimetry to identify PNMT (phenylethanolamine N-methyltransferase) inhibitors.
Resolution2.3 Å
Binding residue
(original residue number in PDB)		Y35 N39 R44 V53 F182 M258
Binding residue
(residue number reindexed from 1)		Y12 N16 R21 V30 F159 M235
Annotation score1
Binding affinityMOAD: Kd=1.8uM
PDBbind-CN: -logKd/Ki=5.74,Kd=1.8uM
Enzymatic activity
Enzyme Commision number 2.1.1.28: phenylethanolamine N-methyltransferase.
Gene Ontology
Molecular Function
GO:0004603 phenylethanolamine N-methyltransferase activity
GO:0005515 protein binding
GO:0008168 methyltransferase activity
Biological Process
GO:0032259 methylation
GO:0042418 epinephrine biosynthetic process
GO:0042423 catecholamine biosynthetic process
Cellular Component
GO:0005829 cytosol

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3kr1, PDBe:3kr1, PDBj:3kr1
PDBsum3kr1
PubMed20642456
UniProtP11086|PNMT_HUMAN Phenylethanolamine N-methyltransferase (Gene Name=PNMT)

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