Structure of PDB 3qbh Chain A Binding Site BS01

Receptor Information
>3qbh Chain A (length=375) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHPF
LHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVRA
NIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHVP
NLFSLQLCGAGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIVRVEING
QDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASSTEKFPDG
FWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQYLRPVE
DVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGFAVSACH
VHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDQBH
InChIInChI=1S/C29H40N2O6S/c1-4-10-31-25(16-37-29(31)34)14-23-11-20(8-9-27(23)32)12-24-17-38(35,36)18-26(28(24)33)30-15-21-6-5-7-22(13-21)19(2)3/h5-9,11,13,19,24-26,28,30,32-33H,4,10,12,14-18H2,1-3H3/t24-,25+,26+,28+/m1/s1
InChIKeyJYNDAPHZRSRSGI-KAHNYGAISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0CCCN1[C@H](COC1=O)Cc2cc(ccc2O)C[C@@H]3CS(=O)(=O)C[C@@H]([C@H]3O)NCc4cccc(c4)C(C)C
CACTVS 3.370CCCN1[CH](COC1=O)Cc2cc(C[CH]3C[S](=O)(=O)C[CH](NCc4cccc(c4)C(C)C)[CH]3O)ccc2O
CACTVS 3.370CCCN1[C@H](COC1=O)Cc2cc(C[C@@H]3C[S](=O)(=O)C[C@H](NCc4cccc(c4)C(C)C)[C@H]3O)ccc2O
OpenEye OEToolkits 1.7.0CCCN1C(COC1=O)Cc2cc(ccc2O)CC3CS(=O)(=O)CC(C3O)NCc4cccc(c4)C(C)C
ACDLabs 12.01O=S2(=O)CC(C(O)C(NCc1cccc(c1)C(C)C)C2)Cc3ccc(O)c(c3)CC4N(C(=O)OC4)CCC
FormulaC29 H40 N2 O6 S
Name(4S)-4-(2-hydroxy-5-{[(3S,4S,5R)-4-hydroxy-1,1-dioxido-5-{[3-(propan-2-yl)benzyl]amino}tetrahydro-2H-thiopyran-3-yl]methyl}benzyl)-3-propyl-1,3-oxazolidin-2-one
ChEMBLCHEMBL1615184
DrugBank
ZINCZINC000064744194
PDB chain3qbh Chain A Residue 387 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3qbh Structure based design, synthesis and SAR of cyclic hydroxyethylamine (HEA) BACE-1 inhibitors.
Resolution2.24 Å
Binding residue
(original residue number in PDB)		S10 G13 D32 G34 S35 Y71 T72 Q73 F108 I110 I126 Y198 D228 G230 T231 T232
Binding residue
(residue number reindexed from 1)		S13 G16 D35 G37 S38 Y74 T75 Q76 F111 I113 I129 Y188 D218 G220 T221 T222
Annotation score1
Binding affinityMOAD: ic50=0.15uM
PDBbind-CN: -logKd/Ki=6.82,IC50=150nM
BindingDB: IC50=150nM
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 D218 T221
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:3qbh, PDBe:3qbh, PDBj:3qbh
PDBsum3qbh
PubMed21388807
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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