Structure of PDB 3l5b Chain A Binding Site BS01

Receptor Information
>3l5b 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
FLHRYYQRQLSSTYRDLRKGVYVPYKWEGELGTDLVSIPHGPNVTVRANI
AAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNL
FSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYY
EVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIK
AASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRIT
ILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRAR
KRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand IDBDO
InChIInChI=1S/C15H20ClN3O/c1-10(2)8-15(3)13(20)19(14(17)18-15)9-11-5-4-6-12(16)7-11/h4-7,10H,8-9H2,1-3H3,(H2,17,18)/t15-/m1/s1
InChIKeySMHLWQCDIJPLEC-OAHLLOKOSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CC(C)C[C]1(C)NC(=N)N(Cc2cccc(Cl)c2)C1=O
OpenEye OEToolkits 1.7.0[H]/N=C\1/N[C@](C(=O)N1Cc2cccc(c2)Cl)(C)CC(C)C
CACTVS 3.352CC(C)C[C@@]1(C)NC(=N)N(Cc2cccc(Cl)c2)C1=O
OpenEye OEToolkits 1.7.0CC(C)CC1(C(=O)N(C(=N)N1)Cc2cccc(c2)Cl)C
FormulaC15 H20 Cl N3 O
Name(2Z,5R)-3-(3-chlorobenzyl)-2-imino-5-methyl-5-(2-methylpropyl)imidazolidin-4-one
ChEMBL
DrugBank
ZINCZINC000045245449
PDB chain3l5b Chain A Residue 1 [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]
PDB3l5b Discovery of Cyclic Acylguanidines as Highly Potent and Selective beta-Site Amyloid Cleaving Enzyme (BACE) Inhibitors: Part I-Inhibitor Design and Validation
Resolution1.8 Å
Binding residue
(original residue number in PDB)		D93 D289 G291
Binding residue
(residue number reindexed from 1)		D36 D229 G231
Annotation score1
Binding affinityMOAD: Kd=123uM
PDBbind-CN: -logKd/Ki=3.91,Kd=123uM
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 D229 T232
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:3l5b, PDBe:3l5b, PDBj:3l5b
PDBsum3l5b
PubMed20043696
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]