Structure of PDB 5i3x Chain A Binding Site BS01

Receptor Information
>5i3x Chain A (length=373) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFL
HRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRAN
IAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPN
LFSLQLCGLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFP
DGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRP
VEDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDE
FRTAAVEGPFVTLDMEDCGYNIP
Ligand information
Ligand ID68J
InChIInChI=1S/C37H39FN4O2/c1-36(2,3)21-22-40-33(43)17-13-28-24-29-23-27(12-16-32(29)41-34(28)39)31-9-5-4-7-25(31)8-6-18-37(19-20-37)42-35(44)26-10-14-30(38)15-11-26/h4-5,7,9-12,14-16,23-24H,13,17-22H2,1-3H3,(H2,39,41)(H,40,43)(H,42,44)
InChIKeyQLQWEADMFLXRFH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01
OpenEye OEToolkits 2.0.4		CC(C)(C)CCNC(=O)CCc1cc2cc(ccc2nc1N)c3ccccc3C#CCC4(CC4)NC(=O)c5ccc(cc5)F
CACTVS 3.385CC(C)(C)CCNC(=O)CCc1cc2cc(ccc2nc1N)c3ccccc3C#CCC4(CC4)NC(=O)c5ccc(F)cc5
FormulaC37 H39 F N4 O2
NameN-(1-{3-[2-(2-amino-3-{3-[(3,3-dimethylbutyl)amino]-3-oxopropyl}quinolin-6-yl)phenyl]prop-2-yn-1-yl}cyclopropyl)-4-fluorobenzamide
ChEMBLCHEMBL3808441
DrugBank
ZINCZINC000584904820
PDB chain5i3x Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5i3x Fragment-Linking Approach Using (19)F NMR Spectroscopy To Obtain Highly Potent and Selective Inhibitors of beta-Secretase.
Resolution1.85 Å
Binding residue
(original residue number in PDB)		G13 D32 G34 V69 Y71 K75 W76 F108 Y198 D228 G230 T232
Binding residue
(residue number reindexed from 1)		G15 D34 G36 V71 Y73 K77 W78 F110 Y190 D220 G222 T224
Annotation score1
Binding affinityMOAD: Kd=8nM
PDBbind-CN: -logKd/Ki=8.10,Kd=8nM
BindingDB: Kd=8.0nM,IC50=191nM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D34 S37 N39 A41 Y73 D220 T223
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:5i3x, PDBe:5i3x, PDBj:5i3x
PDBsum5i3x
PubMed26978477
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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