Structure of PDB 2qmf Chain A Binding Site BS01

Receptor Information
>2qmf 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 IDCS9
InChIInChI=1S/C34H41F2N3O4/c1-4-11-39(12-5-2)34(42)25-14-22(3)13-24(18-25)33(41)38-31(17-23-15-26(35)19-27(36)16-23)32(40)30-20-29(21-37-30)43-28-9-7-6-8-10-28/h6-10,13-16,18-19,29-32,37,40H,4-5,11-12,17,20-21H2,1-3H3,(H,38,41)/t29-,30-,31+,32-/m1/s1
InChIKeyYDCNYSQITCUGST-FEFKUCBWSA-N
SMILES
SoftwareSMILES
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)Oc4ccccc4)O)C
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)Oc4ccccc4
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)Oc4ccccc4
OpenEye OEToolkits 1.5.0CCCN(CCC)C(=O)c1cc(cc(c1)C(=O)NC(Cc2cc(cc(c2)F)F)C(C3CC(CN3)Oc4ccccc4)O)C
ACDLabs 10.04O=C(N(CCC)CCC)c1cc(cc(c1)C)C(=O)NC(Cc2cc(F)cc(F)c2)C(O)C4NCC(Oc3ccccc3)C4
FormulaC34 H41 F2 N3 O4
NameN'-{(1S,2R)-1-(3,5-DIFLUOROBENZYL)-2-HYDROXY-2-[(2R,4R)-4-PHENOXYPYRROLIDIN-2-YL]ETHYL}-5-METHYL-N,N-DIPROPYLISOPHTHALAMIDE
ChEMBLCHEMBL403727
DrugBank
ZINCZINC000016052458
PDB chain2qmf 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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PDB2qmf Potent pyrrolidine- and piperidine-based BACE-1 inhibitors.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		G72 Q73 D93 G95 S96 Y132 T133 Q134 G135 F169 I171 R189 Y259 D289 G291 T293
Binding residue
(residue number reindexed from 1)		G15 Q16 D36 G38 S39 Y75 T76 Q77 G78 F112 I114 R132 Y202 D232 G234 T236
Annotation score1
Binding affinityMOAD: ic50=3nM
PDBbind-CN: -logKd/Ki=8.52,IC50=3nM
BindingDB: IC50=165nM
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:2qmf, PDBe:2qmf, PDBj:2qmf
PDBsum2qmf
PubMed18023580
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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