Structure of PDB 2vj6 Chain A Binding Site BS01

Receptor Information
>2vj6 Chain A (length=370) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHR
YYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPQVTVRANIA
AITESDKFFIQGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLF
SLQLCGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKM
DCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGE
QLVCWQAGTTPWNIFPVISLYLMGEVTQQSFRITILPQQYLRPVEDVATS
QDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEF
RTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDVG5
InChIInChI=1S/C32H45N5O4/c1-3-33-26-18-24(19-27(20-26)37-16-10-15-30(37)39)32(41)36-28(17-23-11-6-4-7-12-23)29(38)21-34-22(2)31(40)35-25-13-8-5-9-14-25/h4,6-7,11-12,18-20,22,25,28-29,33-34,38H,3,5,8-10,13-17,21H2,1-2H3,(H,35,40)(H,36,41)/t22-,28-,29+/m0/s1
InChIKeyARWMRRUIIHCDKG-PWUSVURUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.6.1CCNc1cc(cc(c1)N2CCCC2=O)C(=O)N[C@@H](Cc3ccccc3)[C@@H](CN[C@@H](C)C(=O)NC4CCCCC4)O
OpenEye OEToolkits 1.6.1CCNc1cc(cc(c1)N2CCCC2=O)C(=O)NC(Cc3ccccc3)C(CNC(C)C(=O)NC4CCCCC4)O
CACTVS 3.352CCNc1cc(cc(c1)C(=O)N[CH](Cc2ccccc2)[CH](O)CN[CH](C)C(=O)NC3CCCCC3)N4CCCC4=O
ACDLabs 10.04O=C(NC1CCCCC1)C(NCC(O)C(NC(=O)c2cc(cc(c2)N3C(=O)CCC3)NCC)Cc4ccccc4)C
CACTVS 3.352CCNc1cc(cc(c1)C(=O)N[C@@H](Cc2ccccc2)[C@H](O)CN[C@@H](C)C(=O)NC3CCCCC3)N4CCCC4=O
FormulaC32 H45 N5 O4
Name N-[(1S,2R)-1-benzyl-3-{[(1S)-2-(cyclohexylamino)-1-methyl-2-oxoethyl]amino}-2-hydroxypropyl]-3-(ethylamino)-5-(2-oxopyrrolidin-1-yl)benzamide
ChEMBLCHEMBL251862
DrugBank
ZINCZINC000028978361
PDB chain2vj6 Chain A Residue 1447 [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]
PDB2vj6 Bace-1 Inhibitors Part 2: Identification of Hydroxy Ethylamines (Heas) with Reduced Peptidic Character.
Resolution1.8 Å
Binding residue
(original residue number in PDB)		G72 G74 L91 D93 G95 S96 Y132 T133 Q134 F169 W176 D289 G291 T292 T293 N294 R296 N446
Binding residue
(residue number reindexed from 1)		G11 G13 L30 D32 G34 S35 Y71 T72 Q73 F108 W115 D213 G215 T216 T217 N218 R220 N370
Annotation score1
Binding affinityMOAD: ic50=13nM
PDBbind-CN: -logKd/Ki=7.89,IC50=13nM
BindingDB: IC50=310nM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D32 S35 N37 A39 Y71 D213 T216
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:2vj6, PDBe:2vj6, PDBj:2vj6
PDBsum2vj6
PubMed18166458
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

[Back to BioLiP]