Structure of PDB 3n4l Chain A Binding Site BS01

Receptor Information
>3n4l Chain A (length=375) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGSVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEIN
GQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPD
GFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPV
EDVSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHV
HDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand ID842
InChIInChI=1S/C27H32F2N4O2/c1-19(34)32-25(15-20-13-22(28)17-23(29)14-20)26(35)18-30-27(9-3-2-4-10-27)21-7-5-8-24(16-21)33-12-6-11-31-33/h5-8,11-14,16-17,25-26,30,35H,2-4,9-10,15,18H2,1H3,(H,32,34)/t25-,26+/m0/s1
InChIKeyQXNFPOMRKODYSK-IZZNHLLZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CC(=O)N[C@@H](Cc1cc(cc(c1)F)F)[C@@H](CNC2(CCCCC2)c3cccc(c3)n4cccn4)O
CACTVS 3.370CC(=O)N[C@@H](Cc1cc(F)cc(F)c1)[C@H](O)CNC2(CCCCC2)c3cccc(c3)n4cccn4
ACDLabs 12.01Fc1cc(cc(F)c1)CC(NC(=O)C)C(O)CNC4(c2cccc(c2)n3nccc3)CCCCC4
OpenEye OEToolkits 1.7.0CC(=O)NC(Cc1cc(cc(c1)F)F)C(CNC2(CCCCC2)c3cccc(c3)n4cccn4)O
CACTVS 3.370CC(=O)N[CH](Cc1cc(F)cc(F)c1)[CH](O)CNC2(CCCCC2)c3cccc(c3)n4cccn4
FormulaC27 H32 F2 N4 O2
NameN-[(1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-3-({1-[3-(1H-pyrazol-1-yl)phenyl]cyclohexyl}amino)propyl]acetamide
ChEMBLCHEMBL572081
DrugBank
ZINCZINC000045286908
PDB chain3n4l Chain A Residue 407 [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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PDB3n4l Improving the permeability of the hydroxyethylamine BACE-1 inhibitors: structure-activity relationship of P2' substituents.
Resolution2.7 Å
Binding residue
(original residue number in PDB)		D38 G40 P76 Y77 T78 F114 I132 Y204 I232 D234 G236
Binding residue
(residue number reindexed from 1)		D35 G37 P73 Y74 T75 F111 I129 Y189 I217 D219 G221
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=7.23,IC50=59nM
BindingDB: IC50=59nM
Enzymatic activity
Catalytic site (original residue number in PDB) D38 S41 N43 A45 Y77 D234 T237
Catalytic site (residue number reindexed from 1) D35 S38 N40 A42 Y74 D219 T222
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:3n4l, PDBe:3n4l, PDBj:3n4l
PDBsum3n4l
PubMed20634069
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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