Structure of PDB 2g6p Chain A Binding Site BS03

Receptor Information
>2g6p Chain A (length=304) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
YRYTGKLRPHYPLMPTRPVPSYIQRPDYADHPLGMSESEQALKGTSQIKL
LSSEDIEGMRLVCRLAREVLDVAAGMIKPGVTTEEIDHAVHLACIARNCY
PSPLNYYNFPKSCCTSVNEVICHGIPDRRPLQEGDIVNVDITLYRNGYHG
DLNETFFVGEVDDGARKLVQTTYECLMQAIDAVKPGVRYRELGNIIQKHA
QANGFSVVRSYCGHGIHKLFHTAPNVPHYAKNKAVGVMKSGHVFTIEPMI
CEGGWQDETWPDGWTAVTRDGKRSAQFEHTLLVTDTGCEILTRRLDSARP
HFMS
Ligand information
Ligand IDHM2
InChIInChI=1S/C18H17ClN4/c1-13-16(19)18(21-12-10-14-7-3-2-4-8-14)23-17(22-13)15-9-5-6-11-20-15/h2-9,11H,10,12H2,1H3,(H,21,22,23)
InChIKeyHIUOABSWQSUEGK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04Clc1c(nc(nc1C)c2ncccc2)NCCc3ccccc3
CACTVS 3.341Cc1nc(nc(NCCc2ccccc2)c1Cl)c3ccccn3
OpenEye OEToolkits 1.5.0Cc1c(c(nc(n1)c2ccccn2)NCCc3ccccc3)Cl
FormulaC18 H17 Cl N4
Name5-CHLORO-6-METHYL-N-(2-PHENYLETHYL)-2-PYRIDIN-2-YLPYRIMIDIN-4-AMINE
ChEMBLCHEMBL472879
DrugBankDB07901
ZINCZINC000000108774
PDB chain2g6p Chain A Residue 410 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2g6p Identification of Pyridinylpyrimidines as Inhibitors of Human Methionine Aminopeptidases.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		Y195 C203 H212 Y300 H310 W353
Binding residue
(residue number reindexed from 1)		Y106 C114 H123 Y211 H221 W264
Annotation score1
Binding affinityMOAD: ic50=0.6uM
PDBbind-CN: -logKd/Ki=6.22,IC50=0.6uM
BindingDB: EC50=190nM,IC50=860nM
Enzymatic activity
Catalytic site (original residue number in PDB) D229 D240 H303 H310 E336 E367
Catalytic site (residue number reindexed from 1) D140 D151 H214 H221 E247 E278
Enzyme Commision number 3.4.11.18: methionyl aminopeptidase.
Gene Ontology
Molecular Function
GO:0070006 metalloaminopeptidase activity
Biological Process
GO:0006508 proteolysis

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:2g6p, PDBe:2g6p, PDBj:2g6p
PDBsum2g6p
PubMed16724298
UniProtP53582|MAP11_HUMAN Methionine aminopeptidase 1 (Gene Name=METAP1)

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