Structure of PDB 4ikr Chain A Binding Site BS03

Receptor Information
>4ikr 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 IDPVP
InChIInChI=1S/C16H20ClN5O/c1-12-14(17)16(22-8-6-21(7-9-22)10-11-23)20-15(19-12)13-4-2-3-5-18-13/h2-5,23H,6-11H2,1H3
InChIKeyNLGYGVCRRXIJRR-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.370Cc1nc(nc(N2CCN(CCO)CC2)c1Cl)c3ccccn3
OpenEye OEToolkits 1.7.6Cc1c(c(nc(n1)c2ccccn2)N3CCN(CC3)CCO)Cl
ACDLabs 12.01Clc2c(nc(nc2N1CCN(CCO)CC1)c3ncccc3)C
FormulaC16 H20 Cl N5 O
Name2-{4-[5-chloro-6-methyl-2-(pyridin-2-yl)pyrimidin-4-yl]piperazin-1-yl}ethanol
ChEMBLCHEMBL460432
DrugBank
ZINCZINC000019924596
PDB chain4ikr Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ikr Identification, Biochemical and Structural Evaluation of Species-Specific Inhibitors against Type I Methionine Aminopeptidases
Resolution1.78 Å
Binding residue
(original residue number in PDB)		Y195 Y196 F198 C203 H212 H310 W353
Binding residue
(residue number reindexed from 1)		Y106 Y107 F109 C114 H123 H221 W264
Annotation score1
Binding affinityMOAD: ic50=0.59uM
PDBbind-CN: -logKd/Ki=6.23,IC50=0.59uM
BindingDB: IC50=1100nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:4ikr, PDBe:4ikr, PDBj:4ikr
PDBsum4ikr
PubMed23767698
UniProtP53582|MAP11_HUMAN Methionine aminopeptidase 1 (Gene Name=METAP1)

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