Structure of PDB 3msj Chain A Binding Site BS01

Receptor Information
>3msj Chain A (length=373) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVE
INGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKF
PDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLR
PVEQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVH
DEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDEV3
InChIInChI=1S/C10H12ClN3O/c11-7-2-3-9-8(6-7)13-10(12)14(9)4-1-5-15/h2-3,6,15H,1,4-5H2,(H2,12,13)
InChIKeyNSMVCZCLMLZSOB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01Clc1cc2nc(N)n(c2cc1)CCCO
OpenEye OEToolkits 1.7.0c1cc2c(cc1Cl)nc(n2CCCO)N
CACTVS 3.370Nc1nc2cc(Cl)ccc2n1CCCO
FormulaC10 H12 Cl N3 O
Name3-(2-amino-5-chloro-1H-benzimidazol-1-yl)propan-1-ol
ChEMBLCHEMBL1221922
DrugBank
ZINCZINC000004709834
PDB chain3msj Chain A Residue 393 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3msj Fragment-based discovery and optimization of BACE1 inhibitors.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		D32 G34 Y71 W76 D228
Binding residue
(residue number reindexed from 1)		D36 G38 Y75 W80 D221
Annotation score1
Binding affinityMOAD: ic50=770uM
PDBbind-CN: -logKd/Ki=3.11,IC50=770uM
BindingDB: IC50=770000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D36 S39 N41 A43 Y75 D221 T224
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:3msj, PDBe:3msj, PDBj:3msj
PDBsum3msj
PubMed20656487
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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