Structure of PDB 4ha5 Chain A Binding Site BS01

Receptor Information
>4ha5 Chain A (length=390) 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
RARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand ID13W
InChIInChI=1S/C17H16N4OS/c1-17(8-15(22)21(2)16(19)20-17)14-7-13(10-23-14)12-5-3-4-11(6-12)9-18/h3-7,10H,8H2,1-2H3,(H2,19,20)/t17-/m0/s1
InChIKeyMLNWGLXMDFUREO-KRWDZBQOSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CN1C(=N)N[C](C)(CC1=O)c2scc(c2)c3cccc(c3)C#N
CACTVS 3.370CN1C(=N)N[C@@](C)(CC1=O)c2scc(c2)c3cccc(c3)C#N
OpenEye OEToolkits 1.7.6[H]/N=C/1\N[C@](CC(=O)N1C)(C)c2cc(cs2)c3cccc(c3)C#N
OpenEye OEToolkits 1.7.6CC1(CC(=O)N(C(=N)N1)C)c2cc(cs2)c3cccc(c3)C#N
ACDLabs 12.01O=C3N(C(=[N@H])NC(c2scc(c1cc(C#N)ccc1)c2)(C)C3)C
FormulaC17 H16 N4 O S
Name3-{5-[(2E,4S)-2-imino-1,4-dimethyl-6-oxohexahydropyrimidin-4-yl]thiophen-3-yl}benzonitrile
ChEMBLCHEMBL2151138
DrugBank
ZINCZINC000035965205
PDB chain4ha5 Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4ha5 Design and Validation of Bicyclic Iminopyrimidinones As Beta Amyloid Cleaving Enzyme-1 (BACE1) Inhibitors: Conformational Constraint to Favor a Bioactive Conformation.
Resolution1.83 Å
Binding residue
(original residue number in PDB)		Q73 D93 S96 Y132 W176 D289 G291 T292
Binding residue
(residue number reindexed from 1)		Q16 D36 S39 Y75 W119 D232 G234 T235
Annotation score1
Binding affinityMOAD: Ki=56nM
PDBbind-CN: -logKd/Ki=7.24,Ki=58nM
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:4ha5, PDBe:4ha5, PDBj:4ha5
PDBsum4ha5
PubMed22989333
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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