Structure of PDB 2xfj Chain A Binding Site BS01

Receptor Information
>2xfj Chain A (length=373) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHR
YYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPQVTVRANIA
AITESDKFFIQGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLF
SLQLCASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQD
LKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFW
LGEQLVCWQAGTTPWNIFPVISLYLMGEVTQQSFRITILPQQYLRPVEDV
ATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVH
DEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDVG5
InChIInChI=1S/C32H45N5O4/c1-3-33-26-18-24(19-27(20-26)37-16-10-15-30(37)39)32(41)36-28(17-23-11-6-4-7-12-23)29(38)21-34-22(2)31(40)35-25-13-8-5-9-14-25/h4,6-7,11-12,18-20,22,25,28-29,33-34,38H,3,5,8-10,13-17,21H2,1-2H3,(H,35,40)(H,36,41)/t22-,28-,29+/m0/s1
InChIKeyARWMRRUIIHCDKG-PWUSVURUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1CCNc1cc(cc(c1)N2CCCC2=O)C(=O)N[C@@H](Cc3ccccc3)[C@@H](CN[C@@H](C)C(=O)NC4CCCCC4)O
OpenEye OEToolkits 1.6.1CCNc1cc(cc(c1)N2CCCC2=O)C(=O)NC(Cc3ccccc3)C(CNC(C)C(=O)NC4CCCCC4)O
CACTVS 3.352CCNc1cc(cc(c1)C(=O)N[CH](Cc2ccccc2)[CH](O)CN[CH](C)C(=O)NC3CCCCC3)N4CCCC4=O
ACDLabs 10.04O=C(NC1CCCCC1)C(NCC(O)C(NC(=O)c2cc(cc(c2)N3C(=O)CCC3)NCC)Cc4ccccc4)C
CACTVS 3.352CCNc1cc(cc(c1)C(=O)N[C@@H](Cc2ccccc2)[C@H](O)CN[C@@H](C)C(=O)NC3CCCCC3)N4CCCC4=O
FormulaC32 H45 N5 O4
Name N-[(1S,2R)-1-benzyl-3-{[(1S)-2-(cyclohexylamino)-1-methyl-2-oxoethyl]amino}-2-hydroxypropyl]-3-(ethylamino)-5-(2-oxopyrrolidin-1-yl)benzamide
ChEMBLCHEMBL251862
DrugBank
ZINCZINC000028978361
PDB chain2xfj Chain A Residue 500 [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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PDB2xfj Bace-1 Inhibitors Using Novel Edge-to-Face Interaction with Arg-296
Resolution1.8 Å
Binding residue
(original residue number in PDB)		L91 D93 G95 S96 Y132 T133 Q134 F169 W176 I179 D289 G291 T292 T293 N294 N446
Binding residue
(residue number reindexed from 1)		L30 D32 G34 S35 Y71 T72 Q73 F108 W115 I118 D216 G218 T219 T220 N221 N373
Annotation score1
Binding affinityMOAD: ic50=13nM
PDBbind-CN: -logKd/Ki=7.89,IC50=13nM
BindingDB: IC50=310nM
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 D216 T219
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:2xfj, PDBe:2xfj, PDBj:2xfj
PDBsum2xfj
PubMed20579874
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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