Structure of PDB 3kyr Chain A Binding Site BS01

Receptor Information
>3kyr 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
NLFSLQLCGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEI
NGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEGFW
LGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVDDC
YKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACHVHDEFRTAA
VEGPFVTLDMEDCGY
Ligand information
Ligand ID038
InChIInChI=1S/C34H46N10O8/c1-19(2)15-25(39-30(47)26(20(3)4)40-28(45)24(35)17-36-31(48)27-41-43-44-42-27)29(46)37-18-34(52,14-13-21-9-6-5-7-10-21)33(51)38-23-12-8-11-22(16-23)32(49)50/h5-12,16,19-20,24-26,52H,13-15,17-18,35H2,1-4H3,(H,36,48)(H,37,46)(H,38,51)(H,39,47)(H,40,45)(H,49,50)(H,41,42,43,44)/t24-,25-,26-,34+/m0/s1
InChIKeyFZZOBXKGDCMGAL-NAJARDBOSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)C[C@H](NC(=O)[C@@H](NC(=O)[C@@H](N)CNC(=O)c1[nH]nnn1)C(C)C)C(=O)NC[C@](O)(CCc2ccccc2)C(=O)Nc3cccc(c3)C(O)=O
CACTVS 3.385CC(C)C[CH](NC(=O)[CH](NC(=O)[CH](N)CNC(=O)c1[nH]nnn1)C(C)C)C(=O)NC[C](O)(CCc2ccccc2)C(=O)Nc3cccc(c3)C(O)=O
OpenEye OEToolkits 1.7.5CC(C)C[C@@H](C(=O)NC[C@](CCc1ccccc1)(C(=O)Nc2cccc(c2)C(=O)O)O)NC(=O)[C@H](C(C)C)NC(=O)[C@H](CNC(=O)c3[nH]nnn3)N
OpenEye OEToolkits 1.7.5CC(C)CC(C(=O)NCC(CCc1ccccc1)(C(=O)Nc2cccc(c2)C(=O)O)O)NC(=O)C(C(C)C)NC(=O)C(CNC(=O)c3[nH]nnn3)N
FormulaC34 H46 N10 O8
Name
ChEMBLCHEMBL1229518
DrugBank
ZINCZINC000058638430
PDB chain3kyr Chain A Residue 500 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3kyr Investigation of a-phenylnorstatine and a-benzylnorstatine as transition state isostere motifs in the search for new BACE-1 inhibiotrs
Resolution2.6 Å
Binding residue
(original residue number in PDB)		G34 Y68 P70 Y71 T72 K75 R128 Y198 K224 I226 D228 R235 T329
Binding residue
(residue number reindexed from 1)		G37 Y71 P73 Y74 T75 K78 R131 Y190 K216 I218 D220 R227 T310
Annotation score1
Binding affinityPDBbind-CN: -logKd/Ki=6.72,IC50=0.19uM
BindingDB: IC50=190nM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
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:3kyr, PDBe:3kyr, PDBj:3kyr
PDBsum3kyr
PubMed
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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