Structure of PDB 4r92 Chain A Binding Site BS01

Receptor Information
>4r92 Chain A (length=388) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPH
PFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTV
RANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTH
VPNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRR
EWYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAV
KSIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQS
FRITILPQQYLRPVEDSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRA
RKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand ID3KU
InChIInChI=1S/C25H37N5O2/c1-30-23(32)25(29-24(30)26,13-10-18-6-3-2-4-7-18)17-19-8-5-9-21(16-19)28-22(31)20-11-14-27-15-12-20/h11-12,14-15,18-19,21H,2-10,13,16-17H2,1H3,(H2,26,29)(H,28,31)/t19-,21+,25+/m0/s1
InChIKeyNAGJGYNUXJYJOV-PIBDYAPNSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=N)N[C](CCC2CCCCC2)(C[CH]3CCC[CH](C3)NC(=O)c4ccncc4)C1=O
CACTVS 3.385CN1C(=N)N[C@](CCC2CCCCC2)(C[C@H]3CCC[C@H](C3)NC(=O)c4ccncc4)C1=O
OpenEye OEToolkits 1.7.6[H]/N=C/1\N[C@](C(=O)N1C)(CCC2CCCCC2)C[C@H]3CCC[C@H](C3)NC(=O)c4ccncc4
ACDLabs 12.01O=C1N(C(=[N@H])NC1(CC3CCCC(NC(=O)c2ccncc2)C3)CCC4CCCCC4)C
OpenEye OEToolkits 1.7.6CN1C(=O)C(NC1=N)(CCC2CCCCC2)CC3CCCC(C3)NC(=O)c4ccncc4
FormulaC25 H37 N5 O2
NameN-[(1R,3S)-3-{[(2E,4R)-4-(2-cyclohexylethyl)-2-imino-1-methyl-5-oxoimidazolidin-4-yl]methyl}cyclohexyl]pyridine-4-carboxamide
ChEMBLCHEMBL3354253
DrugBank
ZINCZINC000035861690
PDB chain4r92 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

[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]
PDB4r92 Discovery of potent iminoheterocycle BACE1 inhibitors.
Resolution1.71 Å
Binding residue
(original residue number in PDB)		D93 Y132 K168 F169 F170 R189 D289 G291
Binding residue
(residue number reindexed from 1)		D37 Y76 K112 F113 F114 R133 D233 G235
Annotation score1
Binding affinityMOAD: Ki=39nM
PDBbind-CN: -logKd/Ki=7.41,Ki=39nM
BindingDB: Ki=39nM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D37 S40 N42 A44 Y76 D233 T236
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:4r92, PDBe:4r92, PDBj:4r92
PDBsum4r92
PubMed25455483
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]