Structure of PDB 2qk5 Chain A Binding Site BS01

Receptor Information
>2qk5 Chain A (length=395) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AAGRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVG
AAPHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGP
NVTVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLV
KQTHVPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYT
PIRREWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVF
EAAVKSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEV
TNQSFRITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGF
YVVFDRARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand IDCS5
InChIInChI=1S/C33H41F2N3O4/c1-5-10-38(11-6-2)33(41)26-13-22(3)12-25(18-26)32(40)37-30(17-24-14-27(34)19-28(35)15-24)31(39)21-36-20-23-8-7-9-29(16-23)42-4/h7-9,12-16,18-19,30-31,36,39H,5-6,10-11,17,20-21H2,1-4H3,(H,37,40)/t30-,31+/m0/s1
InChIKeyJEEOUWBWJFSMIP-IOWSJCHKSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)NC(Cc2cc(cc(c2)F)F)C(CNCc3cccc(c3)OC)O)C
CACTVS 3.341CCCN(CCC)C(=O)c1cc(C)cc(c1)C(=O)N[CH](Cc2cc(F)cc(F)c2)[CH](O)CNCc3cccc(OC)c3
ACDLabs 10.04O=C(N(CCC)CCC)c1cc(cc(c1)C(=O)NC(Cc2cc(F)cc(F)c2)C(O)CNCc3cc(OC)ccc3)C
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)N[C@@H](Cc2cc(cc(c2)F)F)[C@@H](CNCc3cccc(c3)OC)O)C
CACTVS 3.341CCCN(CCC)C(=O)c1cc(C)cc(c1)C(=O)N[C@@H](Cc2cc(F)cc(F)c2)[C@H](O)CNCc3cccc(OC)c3
FormulaC33 H41 F2 N3 O4
NameN'-{(1S,2R)-1-(3,5-DIFLUOROBENZYL)-2-HYDROXY-3-[(3-METHOXYBENZYL)AMINO]PROPYL}-5-METHYL-N,N-DIPROPYLISOPHTHALAMIDE
ChEMBLCHEMBL221597
DrugBank
ZINCZINC000003965949
PDB chain2qk5 Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2qk5 Potent pyrrolidine- and piperidine-based BACE-1 inhibitors.
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G72 L91 D93 G95 S96 Y132 T133 Q134 F169 Y259 D289 G291 T293
Binding residue
(residue number reindexed from 1)		G20 L39 D41 G43 S44 Y80 T81 Q82 F117 Y207 D237 G239 T241
Annotation score1
Binding affinityMOAD: ic50=8nM
PDBbind-CN: -logKd/Ki=8.10,IC50=8nM
BindingDB: IC50=20nM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D41 S44 N46 A48 Y80 D237 T240
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:2qk5, PDBe:2qk5, PDBj:2qk5
PDBsum2qk5
PubMed18023580
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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