Structure of PDB 3kmy Chain B Binding Site BS01

Receptor Information
>3kmy Chain B (length=389) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRRE
WYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVK
SIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSF
RITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFD
RARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDD8Y
InChIInChI=1S/C13H13ClN2/c14-12-5-1-3-10(9-12)6-7-11-4-2-8-16-13(11)15/h1-5,8-9H,6-7H2,(H2,15,16)
InChIKeyXJCJGDOLNLEZIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1cc(cc(c1)Cl)CCc2cccnc2N
CACTVS 3.352Nc1ncccc1CCc2cccc(Cl)c2
FormulaC13 H13 Cl N2
Name3-[2-(3-chlorophenyl)ethyl]pyridin-2-amine
ChEMBLCHEMBL575232
DrugBank
ZINC
PDB chain3kmy Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kmy Application of Fragment-Based NMR Screening, X-ray Crystallography, Structure-Based Design, and Focused Chemical Library Design to Identify Novel muM Leads for the Development of nM BACE-1 (beta-Site APP Cleaving Enzyme 1) Inhibitors.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		D93 Y132 G135 K136 F169 D289
Binding residue
(residue number reindexed from 1)		D36 Y75 G78 K79 F112 D232
Annotation score1
Binding affinityMOAD: Kd=32uM
BindingDB: Kd=32nM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D36 S39 N41 A43 Y75 D232 T235
Enzyme Commision number 3.4.23.46: memapsin 2.
Gene Ontology
Molecular Function
GO:0004190 aspartic-type endopeptidase activity
Biological Process
GO:0006508 proteolysis
Cellular Component
GO:0016020 membrane

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:3kmy, PDBe:3kmy, PDBj:3kmy
PDBsum3kmy
PubMed20043700
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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