Structure of PDB 2qmd Chain A Binding Site BS01

Receptor Information
>2qmd Chain A (length=390) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGAGFPLNQSEVLASVGGSMIIGGIDHSLYTGSLWYTPIRRE
WYYEVIIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVK
SIKAASSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSF
RITILPQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFD
RARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand IDCS7
InChIInChI=1S/C35H43F2N3O4/c1-4-11-40(12-5-2)35(43)27-14-23(3)13-26(18-27)34(42)39-32(17-25-15-28(36)19-29(37)16-25)33(41)31-20-30(21-38-31)44-22-24-9-7-6-8-10-24/h6-10,13-16,18-19,30-33,38,41H,4-5,11-12,17,20-22H2,1-3H3,(H,39,42)/t30-,31-,32+,33-/m1/s1
InChIKeyGZHSLBYVXGDJDF-NXVJRICRSA-N
SMILES
SoftwareSMILES
CACTVS 3.341CCCN(CCC)C(=O)c1cc(C)cc(c1)C(=O)N[CH](Cc2cc(F)cc(F)c2)[CH](O)[CH]3C[CH](CN3)OCc4ccccc4
CACTVS 3.341CCCN(CCC)C(=O)c1cc(C)cc(c1)C(=O)N[C@@H](Cc2cc(F)cc(F)c2)[C@H](O)[C@H]3C[C@H](CN3)OCc4ccccc4
ACDLabs 10.04O=C(N(CCC)CCC)c1cc(cc(c1)C(=O)NC(Cc2cc(F)cc(F)c2)C(O)C4NCC(OCc3ccccc3)C4)C
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)NC(Cc2cc(cc(c2)F)F)C(C3CC(CN3)OCc4ccccc4)O)C
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)N[C@@H](Cc2cc(cc(c2)F)F)[C@@H]([C@H]3C[C@H](CN3)OCc4ccccc4)O)C
FormulaC35 H43 F2 N3 O4
NameN'-[(1S,2R)-2-[(2R,4R)-4-(BENZYLOXY)PYRROLIDIN-2-YL]-1-(3,5-DIFLUOROBENZYL)-2-HYDROXYETHYL]-5-METHYL-N,N-DIPROPYLISOPHTHALAMIDE
ChEMBLCHEMBL270359
DrugBank
ZINCZINC000016052459
PDB chain2qmd Chain A Residue 1 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB2qmd Potent pyrrolidine- and piperidine-based BACE-1 inhibitors.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		G72 D93 G95 S96 P131 Y132 T133 Q134 G135 F169 Y259 D289 G291 T293
Binding residue
(residue number reindexed from 1)		G15 D36 G38 S39 P74 Y75 T76 Q77 G78 F112 Y202 D232 G234 T236
Annotation score1
Binding affinityMOAD: ic50=5nM
PDBbind-CN: -logKd/Ki=8.30,IC50=5nM
BindingDB: IC50=150nM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D36 S39 N41 A43 Y75 D232 T235
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:2qmd, PDBe:2qmd, PDBj:2qmd
PDBsum2qmd
PubMed18023580
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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