Structure of PDB 5hdu Chain B Binding Site BS01

Receptor Information
>5hdu Chain B (length=387) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPH
PFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTV
RANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTH
VPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRR
EWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAV
KSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQS
FRITILPQQYLRPVEDSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRA
RKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
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 B 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)		S71 G74 D93 S96 N98 V130 Y132 Q134 W137 I179 D289 G291 T292 T293
Binding residue
(residue number reindexed from 1)		S15 G18 D37 S40 N42 V74 Y76 Q78 W81 I123 D233 G235 T236 T237
Annotation score1
Binding affinityMOAD: 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) D37 S40 N42 A44 Y76 D233 T236
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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