Structure of PDB 4jpe Chain A Binding Site BS01

Receptor Information
>4jpe Chain A (length=402) 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
RARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNIPQTDESRSHH
HH
Ligand information
Ligand ID1M7
InChIInChI=1S/C19H21N5O/c1-18(2)7-13-5-4-12(14-8-21-11-22-9-14)6-15(13)19(10-18)16(25)24(3)17(20)23-19/h4-6,8-9,11H,7,10H2,1-3H3,(H2,20,23)/t19-/m1/s1
InChIKeyUPOMBIAVTOFWMY-LJQANCHMSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1N(C(=NC14c3c(ccc(c2cncnc2)c3)CC(C4)(C)C)N)C
OpenEye OEToolkits 1.7.6CC1(Cc2ccc(cc2[C@]3(C1)C(=O)N(C(=N3)N)C)c4cncnc4)C
OpenEye OEToolkits 1.7.6CC1(Cc2ccc(cc2C3(C1)C(=O)N(C(=N3)N)C)c4cncnc4)C
CACTVS 3.370CN1C(=N[C@@]2(CC(C)(C)Cc3ccc(cc23)c4cncnc4)C1=O)N
CACTVS 3.370CN1C(=N[C]2(CC(C)(C)Cc3ccc(cc23)c4cncnc4)C1=O)N
FormulaC19 H21 N5 O
Name(4R)-2-amino-1,3',3'-trimethyl-7'-(pyrimidin-5-yl)-3',4'-dihydro-2'H-spiro[imidazole-4,1'-naphthalen]-5(1H)-one
ChEMBLCHEMBL2349470
DrugBank
ZINCZINC000095603140
PDB chain4jpe Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4jpe Spirocyclic beta-site amyloid precursor protein cleaving enzyme 1 (BACE1) inhibitors: from hit to lowering of cerebrospinal fluid (CSF) amyloid beta in a higher species.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		Q60 G61 D80 Y119 I158 I166 D276 G278
Binding residue
(residue number reindexed from 1)		Q16 G17 D36 Y75 I114 I122 D232 G234
Annotation score1
Binding affinityMOAD: ic50=48nM
PDBbind-CN: -logKd/Ki=7.32,IC50=48nM
Enzymatic activity
Catalytic site (original residue number in PDB) D80 S83 N85 A87 Y119 D276 T279
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:4jpe, PDBe:4jpe, PDBj:4jpe
PDBsum4jpe
PubMed23537249
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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