Structure of PDB 3cid Chain A Binding Site BS01

Receptor Information
>3cid 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 ID318
InChIInChI=1S/C34H40F2N4O4/c1-4-11-39(12-5-2)33(43)26-14-22(3)13-25(18-26)32(42)38-29(17-24-15-27(35)19-28(36)16-24)31(41)30-34(44)40(21-37-30)20-23-9-7-6-8-10-23/h6-10,13-16,18-19,29-31,37,41H,4-5,11-12,17,20-21H2,1-3H3,(H,38,42)/t29-,30-,31-/m0/s1
InChIKeyHZWNNIVRFLRAQW-CHQNGUEUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)NC(Cc2cc(cc(c2)F)F)C(C3C(=O)N(CN3)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]3NCN(Cc4ccccc4)C3=O
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]3NCN(Cc4ccccc4)C3=O
ACDLabs 10.04O=C(N(CCC)CCC)c1cc(cc(c1)C(=O)NC(Cc2cc(F)cc(F)c2)C(O)C4C(=O)N(Cc3ccccc3)CN4)C
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(CN3)Cc4ccccc4)O)C
FormulaC34 H40 F2 N4 O4
NameN'-[(1S,2S)-2-[(4S)-1-benzyl-5-oxoimidazolidin-4-yl]-1-(3,5-difluorobenzyl)-2-hydroxyethyl]-5-methyl-N,N-dipropylbenzene-1,3-dicarboxamide
ChEMBLCHEMBL507651
DrugBank
ZINCZINC000024975881
PDB chain3cid Chain A Residue 501 [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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PDB3cid Rational design of novel, potent piperazinone and imidazolidinone BACE1 inhibitors
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G72 D93 G95 S96 P131 Y132 T133 Q134 G135 F169 Y259 D289 G291 T293
Binding residue
(residue number reindexed from 1)		G15 D36 G38 S39 P74 Y75 T76 Q77 G78 F112 Y202 D232 G234 T236
Annotation score1
Binding affinityMOAD: ic50=5nM
PDBbind-CN: -logKd/Ki=8.30,IC50=5nM
BindingDB: IC50=5nM
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:3cid, PDBe:3cid, PDBj:3cid
PDBsum3cid
PubMed18468890
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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