Structure of PDB 3cib Chain A Binding Site BS01

Receptor Information
>3cib Chain A (length=390) 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
RARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand ID314
InChIInChI=1S/C36H45F2N3O3/c1-4-13-41(14-5-2)36(44)29-16-24(3)15-28(22-29)35(43)40-33(21-27-18-30(37)23-31(38)19-27)34(42)32-20-26(11-12-39-32)17-25-9-7-6-8-10-25/h6-10,15-16,18-19,22-23,26,32-34,39,42H,4-5,11-14,17,20-21H2,1-3H3,(H,40,43)/t26-,32-,33+,34-/m1/s1
InChIKeyUKXYKYZOSFWZIM-FLQGXGFZSA-N
SMILES
SoftwareSMILES
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[C@H](CCN3)Cc4ccccc4)O)C
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]3C[C@H](CCN3)Cc4ccccc4
ACDLabs 10.04O=C(N(CCC)CCC)c1cc(cc(c1)C)C(=O)NC(Cc2cc(F)cc(F)c2)C(O)C4NCCC(Cc3ccccc3)C4
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)NC(Cc2cc(cc(c2)F)F)C(C3CC(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]3C[CH](CCN3)Cc4ccccc4
FormulaC36 H45 F2 N3 O3
NameN'-[(1S,2R)-2-[(2R,4S)-4-benzylpiperidin-2-yl]-1-(3,5-difluorobenzyl)-2-hydroxyethyl]-5-methyl-N,N-dipropylbenzene-1,3-dicarboxamide
ChEMBLCHEMBL255194
DrugBank
ZINCZINC000024975749
PDB chain3cib Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3cib Rational design of novel, potent piperazinone and imidazolidinone BACE1 inhibitors
Resolution1.72 Å
Binding residue
(original residue number in PDB)		G72 D93 G95 Y132 T133 Q134 F169 Y259 D289 G291 T293
Binding residue
(residue number reindexed from 1)		G15 D36 G38 Y75 T76 Q77 F112 Y202 D232 G234 T236
Annotation score1
Binding affinityMOAD: ic50=14nM
PDBbind-CN: -logKd/Ki=7.85,IC50=14nM
BindingDB: IC50=522nM
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:3cib, PDBe:3cib, PDBj:3cib
PDBsum3cib
PubMed18468890
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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