Structure of PDB 5hdu Chain A Binding Site BS01

Receptor Information
>5hdu Chain A (length=387) 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
RITILPQQYLRPVEDSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRAR
KRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand ID60W
InChIInChI=1S/C23H20FN7O2S/c1-30-20(32)16-10-31(22-27-9-17(24)19(28-22)33-2)12-23(16,29-21(30)26)18-7-15(11-34-18)14-5-3-4-13(6-14)8-25/h3-7,9,11,16H,10,12H2,1-2H3,(H2,26,29)/t16-,23-/m0/s1
InChIKeyUKGROMSNWKWCLS-HJPURHCSSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4CN1C(=O)C2CN(CC2(NC1=N)c3cc(cs3)c4cccc(c4)C#N)c5ncc(c(n5)OC)F
CACTVS 3.385COc1nc(ncc1F)N2C[CH]3C(=O)N(C)C(=N)N[C]3(C2)c4scc(c4)c5cccc(c5)C#N
OpenEye OEToolkits 2.0.4[H]/N=C/1\N[C@]2(CN(C[C@H]2C(=O)N1C)c3ncc(c(n3)OC)F)c4cc(cs4)c5cccc(c5)C#N
CACTVS 3.385COc1nc(ncc1F)N2C[C@H]3C(=O)N(C)C(=N)N[C@]3(C2)c4scc(c4)c5cccc(c5)C#N
ACDLabs 12.01c5(c1cc(C#N)ccc1)cc(C43C(CN(c2ncc(c(n2)OC)F)C3)C(=O)N(\C(=N)N4)C)sc5
FormulaC23 H20 F N7 O2 S
Name3-{5-[(2E,4aR,7aR)-6-(5-fluoro-4-methoxypyrimidin-2-yl)-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl]thiophen-3-yl}benzonitrile
ChEMBLCHEMBL3800286
DrugBank
ZINCZINC000205951475
PDB chain5hdu 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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PDB5hdu Structure-Based Design of an Iminoheterocyclic beta-Site Amyloid Precursor Protein Cleaving Enzyme (BACE) Inhibitor that Lowers Central A beta in Nonhuman Primates.
Resolution1.58 Å
Binding residue
(original residue number in PDB)		G74 D93 S96 N98 V130 T133 Q134 W137 I171 D289 G291 T292
Binding residue
(residue number reindexed from 1)		G17 D36 S39 N41 V73 T76 Q77 W80 I114 D232 G234 T235
Annotation score1
Binding affinityMOAD: Ki=1nM
PDBbind-CN: -logKd/Ki=9.00,Ki=1nM
BindingDB: Ki=1.000000nM,IC50=18nM
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:5hdu, PDBe:5hdu, PDBj:5hdu
PDBsum5hdu
PubMed26937601
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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