Structure of PDB 4h3f Chain B Binding Site BS01

Receptor Information
>4h3f 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 ID10O
InChIInChI=1S/C24H22N6O2S/c1-29-22(31)18-12-30(20-7-4-8-21(27-20)32-2)14-24(18,28-23(29)26)19-10-17(13-33-19)16-6-3-5-15(9-16)11-25/h3-10,13,18H,12,14H2,1-2H3,(H2,26,28)/t18-,24-/m0/s1
InChIKeyDHDYCYIAHXOSEU-UUOWRZLLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.6CN1C(=O)C2CN(CC2(NC1=N)c3cc(cs3)c4cccc(c4)C#N)c5cccc(n5)OC
OpenEye OEToolkits 1.7.6[H]/N=C/1\N[C@]2(CN(C[C@H]2C(=O)N1C)c3cccc(n3)OC)c4cc(cs4)c5cccc(c5)C#N
CACTVS 3.370COc1cccc(n1)N2C[C@H]3C(=O)N(C)C(=N)N[C@]3(C2)c4scc(c4)c5cccc(c5)C#N
CACTVS 3.370COc1cccc(n1)N2C[CH]3C(=O)N(C)C(=N)N[C]3(C2)c4scc(c4)c5cccc(c5)C#N
ACDLabs 12.01O=C4N(C(=[N@H])NC5(c2scc(c1cc(C#N)ccc1)c2)CN(c3nc(OC)ccc3)CC45)C
FormulaC24 H22 N6 O2 S
Name3-{5-[(2E,4aR,7aR)-2-imino-6-(6-methoxypyridin-2-yl)-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophen-3-yl}benzonitrile
ChEMBLCHEMBL2178715
DrugBank
ZINCZINC000095572258
PDB chain4h3f Chain B Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4h3f Design and Validation of Bicyclic Iminopyrimidinones As Beta Amyloid Cleaving Enzyme-1 (BACE1) Inhibitors: Conformational Constraint to Favor a Bioactive Conformation.
Resolution1.7 Å
Binding residue
(original residue number in PDB)		S71 G72 Q73 G74 D93 S96 N98 Y132 W137 F169 I171 I179 D289 G291 T292 T293
Binding residue
(residue number reindexed from 1)		S14 G15 Q16 G17 D36 S39 N41 Y75 W80 F112 I114 I122 D232 G234 T235 T236
Annotation score1
Binding affinityMOAD: Ki=1nM
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:4h3f, PDBe:4h3f, PDBj:4h3f
PDBsum4h3f
PubMed22989333
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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