Structure of PDB 3ixj Chain B Binding Site BS01

Receptor Information
>3ixj Chain B (length=373) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFP
DGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRP
VESQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVH
DEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID586
InChIInChI=1S/C43H51F2N5O9S/c1-26(2)39(43(55)46-24-28-13-9-7-10-14-28)49-42(54)38(58-5)23-37(51)36(25-59-35-21-32(44)20-33(45)22-35)48-41(53)31-17-30(18-34(19-31)50(4)60(6,56)57)40(52)47-27(3)29-15-11-8-12-16-29/h7-22,26-27,36-39,51H,23-25H2,1-6H3,(H,46,55)(H,47,52)(H,48,53)(H,49,54)/t27-,36+,37+,38-,39+/m1/s1
InChIKeyIEIHXPJWOSDLBU-VWMOWEEZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C)C(C(=O)NCc1ccccc1)NC(=O)C(CC(C(COc2cc(cc(c2)F)F)NC(=O)c3cc(cc(c3)N(C)S(=O)(=O)C)C(=O)NC(C)c4ccccc4)O)OC
OpenEye OEToolkits 1.5.0CC(C)[C@@H](C(=O)NCc1ccccc1)NC(=O)[C@@H](C[C@@H]([C@H](COc2cc(cc(c2)F)F)NC(=O)c3cc(cc(c3)N(C)S(=O)(=O)C)C(=O)N[C@H](C)c4ccccc4)O)OC
CACTVS 3.341CO[C@H](C[C@H](O)[C@H](COc1cc(F)cc(F)c1)NC(=O)c2cc(cc(c2)C(=O)N[C@H](C)c3ccccc3)N(C)[S](C)(=O)=O)C(=O)N[C@@H](C(C)C)C(=O)NCc4ccccc4
CACTVS 3.341CO[CH](C[CH](O)[CH](COc1cc(F)cc(F)c1)NC(=O)c2cc(cc(c2)C(=O)N[CH](C)c3ccccc3)N(C)[S](C)(=O)=O)C(=O)N[CH](C(C)C)C(=O)NCc4ccccc4
ACDLabs 10.04O=C(NCc1ccccc1)C(NC(=O)C(OC)CC(O)C(NC(=O)c3cc(C(=O)NC(c2ccccc2)C)cc(N(C)S(=O)(=O)C)c3)COc4cc(F)cc(F)c4)C(C)C
FormulaC43 H51 F2 N5 O9 S
NameN-[4-(1-BENZYLCARBAMOYL-2-METHYL-PROPYLCARBAMOYL)-1-(3,5-DIFLUORO-PHENOXYMETHYL)-2-HYDROXY-4-METHOXY-BUTYL]-5-(METHANES ULFONYL-METHYL-AMINO)-N'-(1-PHENYLETHYL)-ISOPHTHALAMIDE;
N-{(1S,2S,4R)-5-{[(1S)-1-(benzylcarbamoyl)-2-methylpropyl]amino}-1-[(3,5-difluorophenoxy)methyl]-2-hydroxy-4-methoxy-5- oxopentyl}-5-[methyl(methylsulfonyl)amino]-N'-[(1R)-1-phenylethyl]benzene-1,3-dicarboxamide
ChEMBLCHEMBL573106
DrugBank
ZINCZINC000150341140
PDB chain3ixj Chain B Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3ixj Design and Synthesis of Potent and Selective BACE-1 Inhibitors.
Resolution2.2 Å
Binding residue
(original residue number in PDB)
G59 Q60 G61 D80 G82 S83 P118 Y119 T120 Q121 G122 F156 I158 Y246 D276 G278 T279 T280 N281 R283
Binding residue
(residue number reindexed from 1)
G14 Q15 G16 D35 G37 S38 P73 Y74 T75 Q76 G77 F111 I113 Y190 D220 G222 T223 T224 N225 R227
Annotation score1
Binding affinityMOAD: ic50=0.32nM
BindingDB: Ki=<1nM,IC50=0.320000nM
Enzymatic activity
Catalytic site (original residue number in PDB) D80 S83 N85 A87 Y119 D276 T279
Catalytic site (residue number reindexed from 1) D35 S38 N40 A42 Y74 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

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:3ixj, PDBe:3ixj, PDBj:3ixj
PDBsum3ixj
PubMed20128595
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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