Structure of PDB 3skg Chain E Binding Site BS01

Receptor Information
>3skg Chain E (length=386) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
FVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFL
HRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRAN
IAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPN
LFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWY
YEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSI
KAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRI
TILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRA
RKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGY
Ligand information
Ligand IDPB8
InChIInChI=1S/C38H46F2N4O4/c1-24(2)22-38(43-25(3)45)15-16-44(37(38)48)34(14-13-26-9-5-4-6-10-26)36(47)42-33(19-27-17-30(39)21-31(40)18-27)35(46)32-20-28-11-7-8-12-29(28)23-41-32/h4-12,17-18,21,24,32-35,41,46H,13-16,19-20,22-23H2,1-3H3,(H,42,47)(H,43,45)/t32-,33+,34+,35-,38+/m1/s1
InChIKeyJJJDOYFRIVNWHV-WUCUQKTKSA-N
SMILES
SoftwareSMILES
CACTVS 3.370CC(C)C[C@]1(CCN([C@@H](CCc2ccccc2)C(=O)N[C@@H](Cc3cc(F)cc(F)c3)[C@H](O)[C@H]4Cc5ccccc5CN4)C1=O)NC(C)=O
OpenEye OEToolkits 1.7.2CC(C)C[C@]1(CCN(C1=O)[C@@H](CCc2ccccc2)C(=O)N[C@@H](Cc3cc(cc(c3)F)F)[C@@H]([C@H]4Cc5ccccc5CN4)O)NC(=O)C
OpenEye OEToolkits 1.7.2CC(C)CC1(CCN(C1=O)C(CCc2ccccc2)C(=O)NC(Cc3cc(cc(c3)F)F)C(C4Cc5ccccc5CN4)O)NC(=O)C
CACTVS 3.370CC(C)C[C]1(CCN([CH](CCc2ccccc2)C(=O)N[CH](Cc3cc(F)cc(F)c3)[CH](O)[CH]4Cc5ccccc5CN4)C1=O)NC(C)=O
ACDLabs 12.01Fc1cc(cc(F)c1)CC(NC(=O)C(N2C(=O)C(NC(=O)C)(CC2)CC(C)C)CCc3ccccc3)C(O)C5NCc4ccccc4C5
FormulaC38 H46 F2 N4 O4
Name(2S)-2-[(3R)-3-(acetylamino)-3-(2-methylpropyl)-2-oxopyrrolidin-1-yl]-N-{(1R,2S)-3-(3,5-difluorophenyl)-1-hydroxy-1-[(3R)-1,2,3,4-tetrahydroisoquinolin-3-yl]propan-2-yl}-4-phenylbutanamide
ChEMBLCHEMBL1915985
DrugBank
ZINCZINC000082136664
PDB chain3skg Chain E Residue 394 [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]
PDB3skg Synthesis and in vivo evaluation of cyclic diaminopropane BACE-1 inhibitors.
Resolution2.88 Å
Binding residue
(original residue number in PDB)		Q12 G13 L30 D32 G34 Y71 T72 Q73 F108 W115 Y198 D228 G230 T231 T232 R235
Binding residue
(residue number reindexed from 1)		Q14 G15 L32 D34 G36 Y73 T74 Q75 F110 W117 Y200 D230 G232 T233 T234 R237
Annotation score1
Binding affinityBindingDB: IC50=9.5nM
Enzymatic activity
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:3skg, PDBe:3skg, PDBj:3skg
PDBsum3skg
PubMed21974952
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]