Structure of PDB 5hdz Chain A Binding Site BS01

Receptor Information
>5hdz 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 ID954
InChIInChI=1S/C18H18FN7OS2/c1-9-13(19)14(28-3)23-17(22-9)26-7-11-15(27)25(2)16(21)24-18(11,8-26)12-5-4-10(6-20)29-12/h4-5,11H,7-8H2,1-3H3,(H2,21,24)/t11-,18-/m0/s1
InChIKeyRVOBSBJZKQOYEK-VOJFVSQTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.4[H]/N=C/1\N[C@]2(CN(C[C@H]2C(=O)N1C)c3nc(c(c(n3)SC)F)C)c4ccc(s4)C#N
CACTVS 3.385CSc1nc(nc(C)c1F)N2C[CH]3C(=O)N(C)C(=N)N[C]3(C2)c4sc(cc4)C#N
CACTVS 3.385CSc1nc(nc(C)c1F)N2C[C@H]3C(=O)N(C)C(=N)N[C@]3(C2)c4sc(cc4)C#N
OpenEye OEToolkits 2.0.4Cc1c(c(nc(n1)N2CC3C(=O)N(C(=N)NC3(C2)c4ccc(s4)C#N)C)SC)F
ACDLabs 12.01Fc1c(SC)nc(nc1C)N3CC2C(=O)N(C)C(=[N@H])NC2(C3)c4sc(cc4)C#N
FormulaC18 H18 F N7 O S2
Name5-{(2E,4aR,7aR)-6-[5-fluoro-4-methyl-6-(methylsulfanyl)pyrimidin-2-yl]-2-imino-3-methyl-4-oxooctahydro-7aH-pyrrolo[3,4-d]pyrimidin-7a-yl}thiophene-2-carbonitrile
ChEMBLCHEMBL3797680
DrugBank
ZINCZINC000584905511
PDB chain5hdz Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5hdz Structure-Based Design of an Iminoheterocyclic beta-Site Amyloid Precursor Protein Cleaving Enzyme (BACE) Inhibitor that Lowers Central A beta in Nonhuman Primates.
Resolution1.49 Å
Binding residue
(original residue number in PDB)		L91 D93 S96 V130 Y132 W176 I179 R189 D289 G291
Binding residue
(residue number reindexed from 1)		L34 D36 S39 V73 Y75 W119 I122 R132 D232 G234
Annotation score1
Binding affinityMOAD: Ki=45nM
PDBbind-CN: -logKd/Ki=7.35,Ki=45nM
BindingDB: IC50=36nM,Ki=45nM
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:5hdz, PDBe:5hdz, PDBj:5hdz
PDBsum5hdz
PubMed26937601
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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