Structure of PDB 4djx Chain A Binding Site BS01

Receptor Information
>4djx 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 ID0KQ
InChIInChI=1S/C18H17ClN4O/c1-23-16(24)18(13-5-6-13,22-17(23)20)14-4-2-3-11(7-14)12-8-15(19)10-21-9-12/h2-4,7-10,13H,5-6H2,1H3,(H2,20,22)/t18-/m1/s1
InChIKeySZDQNTKTWBPIBH-GOSISDBHSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CN1C(=N)N[C@@](C2CC2)(C1=O)c3cccc(c3)c4cncc(Cl)c4
OpenEye OEToolkits 1.7.6CN1C(=O)C(NC1=N)(c2cccc(c2)c3cc(cnc3)Cl)C4CC4
CACTVS 3.370CN1C(=N)N[C](C2CC2)(C1=O)c3cccc(c3)c4cncc(Cl)c4
OpenEye OEToolkits 1.7.6[H]/N=C/1\N[C@@](C(=O)N1C)(c2cccc(c2)c3cc(cnc3)Cl)C4CC4
ACDLabs 12.01O=C1N(C(=[N@H])NC1(c3cccc(c2cc(Cl)cnc2)c3)C4CC4)C
FormulaC18 H17 Cl N4 O
Name(2E,5R)-5-[3-(5-chloropyridin-3-yl)phenyl]-5-cyclopropyl-2-imino-3-methylimidazolidin-4-one
ChEMBLCHEMBL2011965
DrugBank
ZINCZINC000035825062
PDB chain4djx 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]
PDB4djx Structure based design of iminohydantoin BACE1 inhibitors: Identification of an orally available, centrally active BACE1 inhibitor.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		G72 Q73 G74 D93 S96 Y132 F169 W176 D289 G291 T292
Binding residue
(residue number reindexed from 1)		G15 Q16 G17 D36 S39 Y75 F112 W119 D232 G234 T235
Annotation score1
Binding affinityMOAD: Ki=59nM
PDBbind-CN: -logKd/Ki=7.23,Ki=59nM
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

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4djx, PDBe:4djx, PDBj:4djx
PDBsum4djx
PubMed22390835
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]