Structure of PDB 4r92 Chain B Binding Site BS01

Receptor Information
>4r92 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
FLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRRE
WYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVK
SIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSF
RITILPQQYLRPVEDSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRAR
KRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
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 B Residue 503 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4r92 Discovery of potent iminoheterocycle BACE1 inhibitors.
Resolution1.71 Å
Binding residue
(original residue number in PDB)		D93 K168 F169 F170 W176 D289 G291
Binding residue
(residue number reindexed from 1)		D36 K111 F112 F113 W119 D232 G234
Annotation score1
Binding affinityMOAD: 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) 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:4r92, PDBe:4r92, PDBj:4r92
PDBsum4r92
PubMed25455483
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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