Structure of PDB 3s2o Chain A Binding Site BS01

Receptor Information
>3s2o Chain A (length=377) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFL
HRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRAN
IAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPN
LFSLQLCGAASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFP
DGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRP
VEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSA
CHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDEV6
InChIInChI=1S/C22H29ClN4O/c1-2-17(27-19-4-3-16(23)10-18(19)25-22(27)24)11-20(28)26-21-14-6-12-5-13(8-14)9-15(21)7-12/h3-4,10,12-15,17,21H,2,5-9,11H2,1H3,(H2,24,25)(H,26,28)/t12-,13+,14-,15+,17-,21-/m0/s1
InChIKeyKMAKOMVKNWTGPE-LIXZBVSLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.2CCC(CC(=O)NC1C2CC3CC(C2)CC1C3)n4c5ccc(cc5nc4N)Cl
ACDLabs 12.01O=C(NC3C1CC2CC(C1)CC3C2)CC(n4c5ccc(Cl)cc5nc4N)CC
CACTVS 3.370CC[CH](CC(=O)NC1C2CC3CC(C2)CC1C3)n4c(N)nc5cc(Cl)ccc45
CACTVS 3.370CC[C@@H](CC(=O)NC1C2CC3CC(C2)CC1C3)n4c(N)nc5cc(Cl)ccc45
OpenEye OEToolkits 1.7.2CC[C@@H](CC(=O)NC1C2CC3CC(C2)CC1C3)n4c5ccc(cc5nc4N)Cl
FormulaC22 H29 Cl N4 O
Name(3S)-3-(2-amino-5-chloro-1H-benzimidazol-1-yl)-N-[(1R,3S,5R,7R)-tricyclo[3.3.1.1~3,7~]dec-2-yl]pentanamide
ChEMBL
DrugBank
ZINC
PDB chain3s2o 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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PDB3s2o Fragment-based discovery and optimization of BACE1 inhibitors.
Resolution2.6 Å
Binding residue
(original residue number in PDB)		D32 Y71 W76 D228 G230 N385
Binding residue
(residue number reindexed from 1)		D34 Y73 W78 D220 G222 N377
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=5.05,IC50=8.9uM
BindingDB: IC50=8900nM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D34 S37 N39 A41 Y73 D220 T223
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:3s2o, PDBe:3s2o, PDBj:3s2o
PDBsum3s2o
PubMed20656487
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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