Structure of PDB 3l5e Chain B Binding Site BS01

Receptor Information
>3l5e Chain B (length=386) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYKWEGELGTDLVSIPHGPNVTVRANI
AAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNL
FSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYY
EVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIK
AASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRIT
ILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRAR
KRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDBDW
InChIInChI=1S/C32H49N5O2/c1-2-9-28-23-36(31(39)34-28)21-26-14-16-27(17-15-26)22-37-29(38)32(35-30(37)33,20-25-12-7-4-8-13-25)19-18-24-10-5-3-6-11-24/h14-17,24-25,28H,2-13,18-23H2,1H3,(H2,33,35)(H,34,39)/t28-,32+/m0/s1
InChIKeySILGEXOUELDSRZ-GMCHKSTQSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0[H]/N=C\1/N[C@](C(=O)N1Cc2ccc(cc2)CN3C[C@@H](NC3=O)CCC)(CCC4CCCCC4)CC5CCCCC5
OpenEye OEToolkits 1.7.0CCCC1CN(C(=O)N1)Cc2ccc(cc2)CN3C(=O)C(NC3=N)(CCC4CCCCC4)CC5CCCCC5
CACTVS 3.352CCC[CH]1CN(Cc2ccc(CN3C(=N)N[C](CCC4CCCCC4)(CC5CCCCC5)C3=O)cc2)C(=O)N1
CACTVS 3.352CCC[C@H]1CN(Cc2ccc(CN3C(=N)N[C@](CCC4CCCCC4)(CC5CCCCC5)C3=O)cc2)C(=O)N1
FormulaC32 H49 N5 O2
Name(4S)-1-(4-{[(2Z,4R)-4-(2-cyclohexylethyl)-4-(cyclohexylmethyl)-2-imino-5-oxoimidazolidin-1-yl]methyl}benzyl)-4-propylimidazolidin-2-one
ChEMBLCHEMBL1231280
DrugBank
ZINCZINC000045320343
PDB chain3l5e Chain B Residue 455 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB3l5e Discovery of Cyclic Acylguanidines as Highly Potent and Selective beta-Site Amyloid Cleaving Enzyme (BACE) Inhibitors: Part I-Inhibitor Design and Validation
Resolution1.53 Å
Binding residue
(original residue number in PDB)		Q73 D93 G95 S96 V130 I187 R189 D289 G291 T292 T293
Binding residue
(residue number reindexed from 1)		Q16 D36 G38 S39 V73 I127 R129 D229 G231 T232 T233
Annotation score1
Binding affinityMOAD: ic50=27nM
BindingDB: Ki=27nM
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 D229 T232
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:3l5e, PDBe:3l5e, PDBj:3l5e
PDBsum3l5e
PubMed20043696
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]