Structure of PDB 3ohh Chain A Binding Site BS01

Receptor Information
>3ohh Chain A (length=387) 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
RKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID3HH
InChIInChI=1S/C34H37F2N5O4/c1-4-5-11-40(2)34(44)41-21-29(28-15-22(18-37)9-10-31(28)41)33(43)39-30(16-24-12-25(35)17-26(36)13-24)32(42)20-38-19-23-7-6-8-27(14-23)45-3/h6-10,12-15,17,21,30,32,38,42H,4-5,11,16,19-20H2,1-3H3,(H,39,43)/t30-,32+/m0/s1
InChIKeyZAVRTXWWDAGODB-XDFJSJKPSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCCCN(C)C(=O)n1cc(c2c1ccc(c2)C#N)C(=O)NC(Cc3cc(cc(c3)F)F)C(CNCc4cccc(c4)OC)O
OpenEye OEToolkits 1.7.0CCCCN(C)C(=O)n1cc(c2c1ccc(c2)C#N)C(=O)N[C@@H](Cc3cc(cc(c3)F)F)[C@@H](CNCc4cccc(c4)OC)O
CACTVS 3.370CCCCN(C)C(=O)n1cc(C(=O)N[C@@H](Cc2cc(F)cc(F)c2)[C@H](O)CNCc3cccc(OC)c3)c4cc(ccc14)C#N
CACTVS 3.370CCCCN(C)C(=O)n1cc(C(=O)N[CH](Cc2cc(F)cc(F)c2)[CH](O)CNCc3cccc(OC)c3)c4cc(ccc14)C#N
ACDLabs 12.01Fc1cc(cc(F)c1)CC(NC(=O)c3c2cc(C#N)ccc2n(c3)C(=O)N(CCCC)C)C(O)CNCc4cccc(OC)c4
FormulaC34 H37 F2 N5 O4
NameN~1~-butyl-5-cyano-N~3~-{(1S,2R)-1-(3,5-difluorobenzyl)-2-hydroxy-3-[(3-methoxybenzyl)amino]propyl}-N~1~-methyl-1H-indole-1,3-dicarboxamide
ChEMBL
DrugBank
ZINCZINC000066166239
PDB chain3ohh Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ohh Synthesis and SAR of indole-and 7-azaindole-1,3-dicarboxamide hydroxyethylamine inhibitors of BACE-1.
Resolution2.01 Å
Binding residue
(original residue number in PDB)		G59 D80 G82 Y119 T120 Q121 F156 I158 Y246 D276 G278 T279 T280 R283
Binding residue
(residue number reindexed from 1)		G13 D34 G36 Y73 T74 Q75 F110 I112 Y200 D230 G232 T233 T234 R237
Annotation score1
Binding affinityMOAD: ic50=18nM
PDBbind-CN: -logKd/Ki=7.74,IC50=18nM
Enzymatic activity
Catalytic site (original residue number in PDB) D80 S83 N85 A87 Y119 D276 T279
Catalytic site (residue number reindexed from 1) D34 S37 N39 A41 Y73 D230 T233
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:3ohh, PDBe:3ohh, PDBj:3ohh
PDBsum3ohh
PubMed21078556
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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