Structure of PDB 4r8y Chain A Binding Site BS01

Receptor Information
>4r8y Chain A (length=387) 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
KRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand ID3KO
InChIInChI=1S/C24H40N4O2/c1-27-22(30)24(26-23(27)25,13-11-18-7-3-2-4-8-18)16-20-12-14-28(17-20)21(29)15-19-9-5-6-10-19/h18-20H,2-17H2,1H3,(H2,25,26)/t20-,24-/m1/s1
InChIKeyZROUWOKUKKGJPH-HYBUGGRVSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN1C(=N)N[C@](CCC2CCCCC2)(C[C@H]3CCN(C3)C(=O)CC4CCCC4)C1=O
CACTVS 3.385CN1C(=N)N[C](CCC2CCCCC2)(C[CH]3CCN(C3)C(=O)CC4CCCC4)C1=O
ACDLabs 12.01O=C(N3CCC(CC1(C(=O)N(C(=[N@H])N1)C)CCC2CCCCC2)C3)CC4CCCC4
OpenEye OEToolkits 1.7.6CN1C(=O)C(NC1=N)(CCC2CCCCC2)CC3CCN(C3)C(=O)CC4CCCC4
OpenEye OEToolkits 1.7.6[H]/N=C/1\N[C@](C(=O)N1C)(CCC2CCCCC2)C[C@H]3CCN(C3)C(=O)CC4CCCC4
FormulaC24 H40 N4 O2
Name(2E,5R)-5-(2-cyclohexylethyl)-5-{[(3R)-1-(cyclopentylacetyl)pyrrolidin-3-yl]methyl}-2-imino-3-methylimidazolidin-4-one
ChEMBLCHEMBL3354247
DrugBank
ZINCZINC000137577170
PDB chain4r8y 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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PDB4r8y Discovery of potent iminoheterocycle BACE1 inhibitors.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		D93 Y132 I171 D289 G291
Binding residue
(residue number reindexed from 1)		D36 Y75 I114 D232 G234
Annotation score1
Binding affinityMOAD: Ki=0.64uM
PDBbind-CN: -logKd/Ki=6.19,Ki=0.64uM
BindingDB: Ki=640nM
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:4r8y, PDBe:4r8y, PDBj:4r8y
PDBsum4r8y
PubMed25455483
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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