Structure of PDB 3lnk Chain A Binding Site BS01

Receptor Information
>3lnk 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]
RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPH
PFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTV
RANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTH
VPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRR
EWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAV
KSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQS
FRITILPQQYLRPVEDSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRA
RKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID74A
InChIInChI=1S/C35H42F2N4O4/c1-4-12-40(13-5-2)35(45)27-16-23(3)15-26(20-27)33(43)39-30(19-24-17-28(36)21-29(37)18-24)32(42)31-22-41(14-11-38-31)34(44)25-9-7-6-8-10-25/h6-10,15-18,20-21,30-32,38,42H,4-5,11-14,19,22H2,1-3H3,(H,39,43)/t30-,31+,32-/m0/s1
InChIKeyZJLWDMHHAMNWRK-QAXCHELISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)NC(Cc2cc(cc(c2)F)F)C(C3CN(CCN3)C(=O)c4ccccc4)O)C
CACTVS 3.352CCCN(CCC)C(=O)c1cc(C)cc(c1)C(=O)N[C@@H](Cc2cc(F)cc(F)c2)[C@H](O)[C@H]3CN(CCN3)C(=O)c4ccccc4
OpenEye OEToolkits 1.7.0CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)N[C@@H](Cc2cc(cc(c2)F)F)[C@@H]([C@H]3CN(CCN3)C(=O)c4ccccc4)O)C
CACTVS 3.352CCCN(CCC)C(=O)c1cc(C)cc(c1)C(=O)N[CH](Cc2cc(F)cc(F)c2)[CH](O)[CH]3CN(CCN3)C(=O)c4ccccc4
FormulaC35 H42 F2 N4 O4
NameN'-{(1S,2S)-1-(3,5-difluorobenzyl)-2-hydroxy-2-[(2R)-4-(phenylcarbonyl)piperazin-2-yl]ethyl}-5-methyl-N,N-dipropylbenzene-1,3-dicarboxamide
ChEMBLCHEMBL1097318
DrugBank
ZINCZINC000084466404
PDB chain3lnk 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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PDB3lnk Piperazine sulfonamide BACE1 inhibitors: design, synthesis, and in vivo characterization.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G72 D93 G95 Y132 T133 F169 I171 W176 Y259 D289 G291 T293 T390
Binding residue
(residue number reindexed from 1)		G16 D37 G39 Y76 T77 F113 I115 W120 Y203 D233 G235 T237 T331
Annotation score1
Binding affinityMOAD: ic50=1150nM
PDBbind-CN: -logKd/Ki=5.94,IC50=1150nM
BindingDB: IC50=1150nM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D37 S40 N42 A44 Y76 D233 T236
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:3lnk, PDBe:3lnk, PDBj:3lnk
PDBsum3lnk
PubMed20347593
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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