Structure of PDB 3l5d Chain A Binding Site BS01

Receptor Information
>3l5d Chain A (length=386) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPKWEGELGTDLVSIPHGPNVTVRANIA
AITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLF
SLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYE
VIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKA
ASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITI
LPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARK
RIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand IDBDV
InChIInChI=1S/C21H33N5O2/c1-5-6-11-23-20(28)24-13-16-7-9-17(10-8-16)14-26-18(27)21(4,12-15(2)3)25-19(26)22/h7-10,15H,5-6,11-14H2,1-4H3,(H2,22,25)(H2,23,24,28)/t21-/m1/s1
InChIKeyVPGRKPRUHRVZER-OAQYLSRUSA-N
SMILES
SoftwareSMILES
CACTVS 3.352CCCCNC(=O)NCc1ccc(CN2C(=N)N[C](C)(CC(C)C)C2=O)cc1
CACTVS 3.352CCCCNC(=O)NCc1ccc(CN2C(=N)N[C@](C)(CC(C)C)C2=O)cc1
OpenEye OEToolkits 1.7.0CCCCNC(=O)NCc1ccc(cc1)CN2C(=O)C(NC2=N)(C)CC(C)C
OpenEye OEToolkits 1.7.0[H]/N=C\1/N[C@](C(=O)N1Cc2ccc(cc2)CNC(=O)NCCCC)(C)CC(C)C
FormulaC21 H33 N5 O2
Name1-butyl-3-(4-{[(2Z,4R)-2-imino-4-methyl-4-(2-methylpropyl)-5-oxoimidazolidin-1-yl]methyl}benzyl)urea
ChEMBL
DrugBank
ZINCZINC000045258600
PDB chain3l5d 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]
PDB3l5d Discovery of Cyclic Acylguanidines as Highly Potent and Selective beta-Site Amyloid Cleaving Enzyme (BACE) Inhibitors: Part I-Inhibitor Design and Validation
Resolution1.75 Å
Binding residue
(original residue number in PDB)		D93 D289 G291 T292 T293
Binding residue
(residue number reindexed from 1)		D36 D228 G230 T231 T232
Annotation score1
Binding affinityMOAD: ic50~78000nM
PDBbind-CN: -logKd/Ki=4.11,IC50=78000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 D289 T292
Catalytic site (residue number reindexed from 1) D36 S39 N41 A43 D228 T231
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:3l5d, PDBe:3l5d, PDBj:3l5d
PDBsum3l5d
PubMed20043696
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]