Structure of PDB 3cic Chain B Binding Site BS01

Receptor Information
>3cic Chain B (length=389) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRRE
WYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVK
SIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSF
RITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFD
RARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID316
InChIInChI=1S/C35H42F2N4O4/c1-4-12-40(13-5-2)34(44)27-16-23(3)15-26(20-27)33(43)39-30(19-25-17-28(36)21-29(37)18-25)32(42)31-35(45)41(14-11-38-31)22-24-9-7-6-8-10-24/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
InChIKeyXKXGRRZAMDHVGR-CPCREDONSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCN(CCC)C(=O)c1cc(C)cc(c1)C(=O)N[C@@H](Cc2cc(F)cc(F)c2)[C@H](O)[C@@H]3NCCN(Cc4ccccc4)C3=O
ACDLabs 10.04O=C(N(CCC)CCC)c1cc(cc(c1)C)C(=O)NC(Cc2cc(F)cc(F)c2)C(O)C4C(=O)N(Cc3ccccc3)CCN4
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)N[C@@H](Cc2cc(cc(c2)F)F)[C@@H]([C@H]3C(=O)N(CCN3)Cc4ccccc4)O)C
CACTVS 3.341CCCN(CCC)C(=O)c1cc(C)cc(c1)C(=O)N[CH](Cc2cc(F)cc(F)c2)[CH](O)[CH]3NCCN(Cc4ccccc4)C3=O
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)NC(Cc2cc(cc(c2)F)F)C(C3C(=O)N(CCN3)Cc4ccccc4)O)C
FormulaC35 H42 F2 N4 O4
NameN'-[(1S,2S)-2-[(2S)-4-benzyl-3-oxopiperazin-2-yl]-1-(3,5-difluorobenzyl)-2-hydroxyethyl]-5-methyl-N,N-dipropylbenzene-1,3-dicarboxamide
ChEMBLCHEMBL509210
DrugBank
ZINCZINC000024975929
PDB chain3cic Chain B Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3cic Rational design of novel, potent piperazinone and imidazolidinone BACE1 inhibitors
Resolution1.75 Å
Binding residue
(original residue number in PDB)		G72 Q73 D93 G95 S96 Y132 T133 Q134 G135 F169 I171 Y259 D289 G291 T293
Binding residue
(residue number reindexed from 1)		G15 Q16 D36 G38 S39 Y75 T76 Q77 G78 F112 I114 Y202 D232 G234 T236
Annotation score1
Binding affinityMOAD: ic50=3nM
BindingDB: IC50=300nM,Ki=3nM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D36 S39 N41 A43 Y75 D232 T235
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:3cic, PDBe:3cic, PDBj:3cic
PDBsum3cic
PubMed18468890
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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