Structure of PDB 3fkt Chain A Binding Site BS01

Receptor Information
>3fkt Chain A (length=368) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYTQGAWAGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGAVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFP
DGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRP
VSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHDEF
RTAAVEGPFVTLDMEDCG
Ligand information
Ligand IDSII
InChIInChI=1S/C28H34FN5O2/c1-20(35)30-24-12-10-21(11-13-24)19-33-16-14-28(15-17-33)26(31-23-7-3-2-4-8-23)32-27(36)34(28)25-9-5-6-22(29)18-25/h5-6,9-13,18,23H,2-4,7-8,14-17,19H2,1H3,(H,30,35)(H,31,32,36)
InChIKeyVXIOVOURIXSOTD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(=O)Nc1ccc(cc1)CN2CCC3(CC2)C(=NC(=O)N3c4cccc(c4)F)NC5CCCCC5
ACDLabs 10.04Fc5cccc(N2C(=O)N=C(NC1CCCCC1)C23CCN(CC3)Cc4ccc(NC(=O)C)cc4)c5
CACTVS 3.341CC(=O)Nc1ccc(CN2CCC3(CC2)N(C(=O)N=C3NC4CCCCC4)c5cccc(F)c5)cc1
FormulaC28 H34 F N5 O2
NameN-(4-{[4-(cyclohexylamino)-1-(3-fluorophenyl)-2-oxo-1,3,8-triazaspiro[4.5]dec-3-en-8-yl]methyl}phenyl)acetamide
ChEMBLCHEMBL495087
DrugBank
ZINCZINC000039470958
PDB chain3fkt Chain A Residue 406 [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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PDB3fkt Discovery and X-ray Crystallographic Analysis of a Iminohydantoin Inhibitor of beta-Secretase
Resolution1.9 Å
Binding residue
(original residue number in PDB)		L50 Y91 T92 Q93 G94 F128 I130 Y218 G250 T349
Binding residue
(residue number reindexed from 1)		L34 Y75 T76 Q77 G78 F112 I114 Y190 G222 T316
Annotation score1
Binding affinityMOAD: ic50=2.8uM
PDBbind-CN: -logKd/Ki=5.55,IC50=2.8uM
BindingDB: IC50=2800nM
Enzymatic activity
Catalytic site (original residue number in PDB) D52 S55 N57 A59 Y91 D248 T251
Catalytic site (residue number reindexed from 1) D36 S39 N41 A43 Y75 D220 T223
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:3fkt, PDBe:3fkt, PDBj:3fkt
PDBsum3fkt
PubMed18811140
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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