Structure of PDB 3l3a Chain A Binding Site BS01

Receptor Information
>3l3a Chain A (length=365) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGAGVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIV
RVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASST
EKFPDGFWLGEQLVCWQTPWNIFPVISLYLMGEVTNQSFRITILPQQYLR
PVCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFR
TAAVEGPFVTLDCGY
Ligand information
Ligand ID625
InChIInChI=1S/C26H23ClN4O/c27-23-8-2-1-7-22(23)25-15-14-24(31(25)18-20-6-5-9-26(29)30-20)19-10-12-21(13-11-19)32-17-4-3-16-28/h1-2,5-15H,3-4,17-18H2,(H2,29,30)
InChIKeyCERJQPWNRISSQS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.352Nc1cccc(Cn2c(ccc2c3ccccc3Cl)c4ccc(OCCCC#N)cc4)n1
OpenEye OEToolkits 1.7.0c1ccc(c(c1)c2ccc(n2Cc3cccc(n3)N)c4ccc(cc4)OCCCC#N)Cl
FormulaC26 H23 Cl N4 O
Name4-(4-{1-[(6-aminopyridin-2-yl)methyl]-5-(2-chlorophenyl)-1H-pyrrol-2-yl}phenoxy)butanenitrile
ChEMBLCHEMBL1089137
DrugBank
ZINCZINC000034642784
PDB chain3l3a Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3l3a Novel pyrrolyl 2-aminopyridines as potent and selective human beta-secretase (BACE1) inhibitors.
Resolution2.362 Å
Binding residue
(original residue number in PDB)		G73 Q74 G75 L92 D94 V131 Y133 W138 F170 I172 W177 I180 R190 D290 G292 T294
Binding residue
(residue number reindexed from 1)		G14 Q15 G16 L33 D35 V72 Y74 W79 F111 I113 W118 I121 R131 D224 G226 T228
Annotation score1
Binding affinityMOAD: ic50=0.42uM
PDBbind-CN: -logKd/Ki=6.38,IC50=0.42uM
BindingDB: IC50=420nM
Enzymatic activity
Catalytic site (original residue number in PDB) D94 S97 N99 A101 Y133 D290 T293
Catalytic site (residue number reindexed from 1) D35 S38 N40 A42 Y74 D224 T227
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:3l3a, PDBe:3l3a, PDBj:3l3a
PDBsum3l3a
PubMed20223661
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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