Structure of PDB 2vj9 Chain A Binding Site BS01

Receptor Information
>2vj9 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]
EMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPFLHR
YYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPQVTVRANIA
AITESDKFFIQGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVPNLF
SLQLCGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEINGQDLKM
DCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDGFWLGE
QLVCWQAGTTPWNIFPVISLYLMGEVTQQSFRITILPQQYLRPVEDVATS
QDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEF
RTAAVEGPFVTLDMEDCGYNIPQT
Ligand information
Ligand IDVG7
InChIInChI=1S/C29H40N4O3/c1-2-30-24-17-22(18-25(19-24)33-15-9-14-28(33)35)29(36)32-26(16-21-10-5-3-6-11-21)27(34)20-31-23-12-7-4-8-13-23/h3,5-6,10-11,17-19,23,26-27,30-31,34H,2,4,7-9,12-16,20H2,1H3,(H,32,36)/t26-,27+/m0/s1
InChIKeyPVDHVIVUNLQJLY-RRPNLBNLSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCNc1cc(cc(c1)C(=O)N[C@@H](Cc2ccccc2)[C@H](O)CNC3CCCCC3)N4CCCC4=O
ACDLabs 10.04O=C(NC(Cc1ccccc1)C(O)CNC2CCCCC2)c3cc(cc(c3)N4C(=O)CCC4)NCC
OpenEye OEToolkits 1.5.0CCNc1cc(cc(c1)N2CCCC2=O)C(=O)N[C@@H](Cc3ccccc3)[C@@H](CNC4CCCCC4)O
CACTVS 3.341CCNc1cc(cc(c1)C(=O)N[CH](Cc2ccccc2)[CH](O)CNC3CCCCC3)N4CCCC4=O
OpenEye OEToolkits 1.5.0CCNc1cc(cc(c1)N2CCCC2=O)C(=O)NC(Cc3ccccc3)C(CNC4CCCCC4)O
FormulaC29 H40 N4 O3
NameN-[(1S,2R)-1-benzyl-3-(cyclohexylamino)-2-hydroxypropyl]-3-(ethylamino)-5-(2-oxopyrrolidin-1-yl)benzamide
ChEMBLCHEMBL252057
DrugBank
ZINCZINC000013133641
PDB chain2vj9 Chain A Residue 1452 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vj9 Bace-1 Inhibitors Part 2: Identification of Hydroxy Ethylamines (Heas) with Reduced Peptidic Character.
Resolution1.6 Å
Binding residue
(original residue number in PDB)		G74 L91 D93 G95 Y132 T133 Q134 F169 W176 Y259 D289 G291 T292 T293 N294 T450
Binding residue
(residue number reindexed from 1)		G13 L30 D32 G34 Y71 T72 Q73 F108 W115 Y183 D213 G215 T216 T217 N218 T374
Annotation score1
Binding affinityMOAD: ic50=180nM
PDBbind-CN: -logKd/Ki=6.74,IC50=180nM
BindingDB: IC50=180nM
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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:2vj9, PDBe:2vj9, PDBj:2vj9
PDBsum2vj9
PubMed18166458
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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