Structure of PDB 2wf3 Chain A Binding Site BS01

Receptor Information
>2wf3 Chain A (length=374) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHR
YYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPQVTVRANIA
AITESDKFFIQGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLF
SLQLCGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQ
DLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGF
WLGEQLVCWQAGTTPWNIFPVISLYLMGEVTQQSFRITILPQQYLRPVED
VATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHV
HDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDZY3
InChIInChI=1S/C31H40N4O5S/c1-4-33-27-18-24(19-29-26(27)14-9-15-41(38,39)35(29)2)31(37)34-28(17-22-10-6-5-7-11-22)30(36)21-32-20-23-12-8-13-25(16-23)40-3/h5-8,10-13,16,18-19,28,30,32-33,36H,4,9,14-15,17,20-21H2,1-3H3,(H,34,37)/t28-,30+/m0/s1
InChIKeyJAQQVYMOVUUAHB-MFMCTBQISA-N
SMILES
SoftwareSMILES
CACTVS 3.352CCNc1cc(cc2N(C)[S](=O)(=O)CCCc12)C(=O)N[CH](Cc3ccccc3)[CH](O)CNCc4cccc(OC)c4
CACTVS 3.352CCNc1cc(cc2N(C)[S](=O)(=O)CCCc12)C(=O)N[C@@H](Cc3ccccc3)[C@H](O)CNCc4cccc(OC)c4
OpenEye OEToolkits 1.6.1CCNc1cc(cc2c1CCCS(=O)(=O)N2C)C(=O)N[C@@H](Cc3ccccc3)[C@@H](CNCc4cccc(c4)OC)O
ACDLabs 10.04O=C(c1cc2c(c(NCC)c1)CCCS(=O)(=O)N2C)NC(Cc3ccccc3)C(O)CNCc4cccc(OC)c4
OpenEye OEToolkits 1.6.1CCNc1cc(cc2c1CCCS(=O)(=O)N2C)C(=O)NC(Cc3ccccc3)C(CNCc4cccc(c4)OC)O
FormulaC31 H40 N4 O5 S
NameN-{(1S,2R)-1-BENZYL-2-HYDROXY-3-[(3-METHOXYBENZYL)AMINO]PROPYL}-6-(ETHYLAMINO)-1-METHYL-1,3,4,5-TETRAHYDRO-2,1-BENZOTHIAZEPINE-8-CARBOXAMIDE 2,2-DIOXIDE
ChEMBL
DrugBank
ZINCZINC000038998991
PDB chain2wf3 Chain A Residue 2000 [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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PDB2wf3 Second Generation of Bace-1 Inhibitors Part 2: Optimisation of the Non-Prime Side Substituent.
Resolution2.08 Å
Binding residue
(original residue number in PDB)		G72 Q73 L91 D93 G95 Y132 T133 Q134 F169 D289 G291 T292 T293 N294 R296 N446
Binding residue
(residue number reindexed from 1)		G11 Q12 L30 D32 G34 Y71 T72 Q73 F108 D217 G219 T220 T221 N222 R224 N374
Annotation score1
Binding affinityMOAD: ic50=0.019uM
PDBbind-CN: -logKd/Ki=7.72,IC50=19nM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D32 S35 N37 A39 Y71 D217 T220
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:2wf3, PDBe:2wf3, PDBj:2wf3
PDBsum2wf3
PubMed19477642
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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