Structure of PDB 5i3v Chain A Binding Site BS01

Receptor Information
>5i3v Chain A (length=370) 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
VDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFR
TAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand ID68M
InChIInChI=1S/C25H32N4O/c1-16-7-6-11-27-22(16)18-8-9-21-19(14-18)15-20(23(26)29-21)13-17(2)24(30)28-12-10-25(3,4)5/h6-9,11,14-15,17H,10,12-13H2,1-5H3,(H2,26,29)(H,28,30)/t17-/m1/s1
InChIKeyZVOWIRUWKAUSAB-QGZVFWFLSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[C@H](Cc1cc2cc(ccc2nc1N)c3ncccc3C)C(=O)NCCC(C)(C)C
ACDLabs 12.01CC(C)(C)CCNC(=O)C(C)Cc1cc2cc(ccc2nc1N)c3c(cccn3)C
OpenEye OEToolkits 2.0.4Cc1cccnc1c2ccc3c(c2)cc(c(n3)N)C[C@@H](C)C(=O)NCCC(C)(C)C
OpenEye OEToolkits 2.0.4Cc1cccnc1c2ccc3c(c2)cc(c(n3)N)CC(C)C(=O)NCCC(C)(C)C
CACTVS 3.385C[CH](Cc1cc2cc(ccc2nc1N)c3ncccc3C)C(=O)NCCC(C)(C)C
FormulaC25 H32 N4 O
Name(2R)-3-[2-amino-6-(3-methylpyridin-2-yl)quinolin-3-yl]-N-(3,3-dimethylbutyl)-2-methylpropanamide
ChEMBLCHEMBL1821826
DrugBank
ZINCZINC000072179707
PDB chain5i3v Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5i3v Fragment-Linking Approach Using (19)F NMR Spectroscopy To Obtain Highly Potent and Selective Inhibitors of beta-Secretase.
Resolution1.62 Å
Binding residue
(original residue number in PDB)		D32 G34 Y71 K75 W76 F108 D228
Binding residue
(residue number reindexed from 1)		D34 G36 Y73 K77 W78 F110 D220
Annotation score1
Binding affinityMOAD: Kd=16nM
PDBbind-CN: -logKd/Ki=7.80,Kd=16nM
BindingDB: IC50=16nM
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:5i3v, PDBe:5i3v, PDBj:5i3v
PDBsum5i3v
PubMed26978477
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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