Structure of PDB 3kmx Chain B Binding Site BS01

Receptor Information
>3kmx 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 IDG00
InChIInChI=1S/C12H17ClN2OS/c1-2-3-6-16-11-5-4-9(7-10(11)13)8-17-12(14)15/h4-5,7H,2-3,6,8H2,1H3,(H3,14,15)
InChIKeyIONZMLSFEITLRK-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCCCOc1ccc(cc1Cl)CSC(=N)N
OpenEye OEToolkits 1.7.0[H]/N=C(/N)\SCc1ccc(c(c1)Cl)OCCCC
CACTVS 3.352CCCCOc1ccc(CSC(N)=N)cc1Cl
FormulaC12 H17 Cl N2 O S
Name4-butoxy-3-chlorobenzyl imidothiocarbamate
ChEMBLCHEMBL568966
DrugBank
ZINCZINC000004713685
PDB chain3kmx 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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PDB3kmx 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.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		Q73 D93 G95 Y132 Q134 G135 D289 G291
Binding residue
(residue number reindexed from 1)		Q16 D36 G38 Y75 Q77 G78 D232 G234
Annotation score1
Binding affinityMOAD: Kd=15uM
BindingDB: Kd=15nM,IC50=200nM
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:3kmx, PDBe:3kmx, PDBj:3kmx
PDBsum3kmx
PubMed20043700
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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