Structure of PDB 4djw Chain A Binding Site BS01

Receptor Information
>4djw Chain A (length=390) 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
RARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand ID0KP
InChIInChI=1S/C21H18N4O/c1-25-19(26)21(24-20(25)22,17-9-3-2-4-10-17)18-11-5-7-15(13-18)16-8-6-12-23-14-16/h2-14H,1H3,(H2,22,24)/t21-/m1/s1
InChIKeyPNSQCPQDRVOKMA-OAQYLSRUSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CN1C(=N)N[C@](C1=O)(c2ccccc2)c3cccc(c3)c4cccnc4
OpenEye OEToolkits 1.7.6[H]/N=C/1\N[C@](C(=O)N1C)(c2ccccc2)c3cccc(c3)c4cccnc4
CACTVS 3.370CN1C(=N)N[C](C1=O)(c2ccccc2)c3cccc(c3)c4cccnc4
ACDLabs 12.01O=C3N(C(=[N@H])NC3(c2cc(c1cccnc1)ccc2)c4ccccc4)C
OpenEye OEToolkits 1.7.6CN1C(=O)C(NC1=N)(c2ccccc2)c3cccc(c3)c4cccnc4
FormulaC21 H18 N4 O
Name(2E,5R)-2-imino-3-methyl-5-phenyl-5-[3-(pyridin-3-yl)phenyl]imidazolidin-4-one
ChEMBLCHEMBL2011983
DrugBank
ZINCZINC000034503925
PDB chain4djw 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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PDB4djw Structure based design of iminohydantoin BACE1 inhibitors: Identification of an orally available, centrally active BACE1 inhibitor.
Resolution1.9 Å
Binding residue
(original residue number in PDB)		G72 G74 L91 D93 S96 Y132 F169 I171 W176 I179 D289 G291
Binding residue
(residue number reindexed from 1)		G15 G17 L34 D36 S39 Y75 F112 I114 W119 I122 D232 G234
Annotation score1
Binding affinityMOAD: Ki=0.53uM
PDBbind-CN: -logKd/Ki=6.28,Ki=0.53uM
BindingDB: IC50=1680nM
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:4djw, PDBe:4djw, PDBj:4djw
PDBsum4djw
PubMed22390835
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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