Structure of PDB 1w51 Chain A Binding Site BS01

Receptor Information
>1w51 Chain A (length=374) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFL
HRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRAN
IAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPN
LFSLQLCGAASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFP
DGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRP
VETSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHV
HDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDL01
InChIInChI=1S/C32H41N3O4/c1-4-17-35(18-5-2)32(38)27-15-10-14-26(21-27)31(37)34-29(20-24-11-7-6-8-12-24)30(36)23-33-22-25-13-9-16-28(19-25)39-3/h6-16,19,21,29-30,33,36H,4-5,17-18,20,22-23H2,1-3H3,(H,34,37)/t29-,30+/m0/s1
InChIKeyWPRACYICKOKGTO-XZWHSSHBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cccc(c1)C(=O)NC(Cc2ccccc2)C(CNCc3cccc(c3)OC)O
CACTVS 3.341CCCN(CCC)C(=O)c1cccc(c1)C(=O)N[CH](Cc2ccccc2)[CH](O)CNCc3cccc(OC)c3
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cccc(c1)C(=O)N[C@@H](Cc2ccccc2)[C@@H](CNCc3cccc(c3)OC)O
ACDLabs 10.04O=C(N(CCC)CCC)c1cccc(c1)C(=O)NC(Cc2ccccc2)C(O)CNCc3cc(OC)ccc3
CACTVS 3.341CCCN(CCC)C(=O)c1cccc(c1)C(=O)N[C@@H](Cc2ccccc2)[C@H](O)CNCc3cccc(OC)c3
FormulaC32 H41 N3 O4
Name3-[({(1S,2R)-1-BENZYL-2-HYDROXY-3-[(3-METHOXYBENZYL)AMINO]PROPYL}AMINO)(HYDROXY)METHYL]-N,N-DIPROPYLBENZAMIDE;
HYDROXYETHYLAMINE BACE INHIBITOR
ChEMBLCHEMBL443239
DrugBank
ZINCZINC000028968529
PDB chain1w51 Chain A Residue 1506 [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]
PDB1w51 Apo and Inhibitor Complex Structures of Bace (Beta-Secretase)
Resolution2.55 Å
Binding residue
(original residue number in PDB)		G11 G13 D32 G34 S35 P70 Y71 T72 Q73 F108 R128 Y198 D228 G230 T232
Binding residue
(residue number reindexed from 1)		G13 G15 D34 G36 S37 P72 Y73 T74 Q75 F110 R130 Y190 D220 G222 T224
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.30,IC50=500nM
BindingDB: IC50=500nM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D34 S37 N39 A41 Y73 D220 T223
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:1w51, PDBe:1w51, PDBj:1w51
PDBsum1w51
PubMed15451669
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]