Structure of PDB 5i3y Chain A Binding Site BS01

Receptor Information
>5i3y Chain A (length=369) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFL
HRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRAN
IAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPN
LFSLQLCGALASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVE
INGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKF
PDGFWLGEQLVCWTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVED
VDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFR
TAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID68K
InChIInChI=1S/C38H40FN5O2/c1-38(2,3)20-21-41-35(45)19-12-28-23-29-22-27(11-18-34(29)44-36(28)40)33-7-5-4-6-25(33)10-15-31-16-17-32(24-42-31)43-37(46)26-8-13-30(39)14-9-26/h4-9,11,13-14,16-18,22-24H,10,12,15,19-21H2,1-3H3,(H2,40,44)(H,41,45)(H,43,46)
InChIKeyRTOUKFMBOVMEOT-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)(C)CCNC(=O)CCc1cc2cc(ccc2nc1N)c3ccccc3CCc4ccc(NC(=O)c5ccc(F)cc5)cn4
ACDLabs 12.01CC(CCNC(CCc1c(N)nc2c(c1)cc(cc2)c3c(cccc3)CCc4ccc(cn4)NC(c5ccc(cc5)F)=O)=O)(C)C
OpenEye OEToolkits 2.0.4CC(C)(C)CCNC(=O)CCc1cc2cc(ccc2nc1N)c3ccccc3CCc4ccc(cn4)NC(=O)c5ccc(cc5)F
FormulaC38 H40 F N5 O2
NameN-(6-{2-[2-(2-amino-3-{3-[(3,3-dimethylbutyl)amino]-3-oxopropyl}quinolin-6-yl)phenyl]ethyl}pyridin-3-yl)-4-fluorobenzamide
ChEMBLCHEMBL3809870
DrugBank
ZINCZINC000584904838
PDB chain5i3y 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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PDB5i3y Fragment-Linking Approach Using (19)F NMR Spectroscopy To Obtain Highly Potent and Selective Inhibitors of beta-Secretase.
Resolution2.15 Å
Binding residue
(original residue number in PDB)		G11 Q12 G13 D32 G34 V69 Y71 K75 W76 F108 I118 R128 Y198 D228 S229 G230 T232
Binding residue
(residue number reindexed from 1)		G13 Q14 G15 D34 G36 V71 Y73 K77 W78 F110 I120 R130 Y191 D221 S222 G223 T225
Annotation score1
Binding affinityMOAD: Kd=0.4nM
PDBbind-CN: -logKd/Ki=9.40,Kd=0.4nM
BindingDB: IC50=16nM,Kd=0.400000nM
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 D221 T224
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:5i3y, PDBe:5i3y, PDBj:5i3y
PDBsum5i3y
PubMed26978477
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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