Structure of PDB 2qmg Chain A Binding Site BS01

Receptor Information
>2qmg 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 IDSC6
InChIInChI=1S/C34H39F2N3O5/c1-21-11-23(16-24(12-21)34(42)39-10-6-7-27(39)20-43-2)33(41)38-31(15-22-13-25(35)17-26(36)14-22)32(40)30-18-29(19-37-30)44-28-8-4-3-5-9-28/h3-5,8-9,11-14,16-17,27,29-32,37,40H,6-7,10,15,18-20H2,1-2H3,(H,38,41)/t27-,29-,30-,31+,32-/m1/s1
InChIKeyKYHYNSQLYDXSNK-MXWGZHRFSA-N
SMILES
SoftwareSMILES
CACTVS 3.341COC[CH]1CCCN1C(=O)c2cc(C)cc(c2)C(=O)N[CH](Cc3cc(F)cc(F)c3)[CH](O)[CH]4C[CH](CN4)Oc5ccccc5
CACTVS 3.341COC[C@H]1CCCN1C(=O)c2cc(C)cc(c2)C(=O)N[C@@H](Cc3cc(F)cc(F)c3)[C@H](O)[C@H]4C[C@H](CN4)Oc5ccccc5
ACDLabs 10.04O=C(N1CCCC1COC)c2cc(cc(c2)C)C(=O)NC(Cc3cc(F)cc(F)c3)C(O)C5NCC(Oc4ccccc4)C5
OpenEye OEToolkits 1.5.0Cc1cc(cc(c1)C(=O)N2CCCC2COC)C(=O)NC(Cc3cc(cc(c3)F)F)C(C4CC(CN4)Oc5ccccc5)O
OpenEye OEToolkits 1.5.0Cc1cc(cc(c1)C(=O)N2CCC[C@@H]2COC)C(=O)N[C@@H](Cc3cc(cc(c3)F)F)[C@@H]([C@H]4C[C@H](CN4)Oc5ccccc5)O
FormulaC34 H39 F2 N3 O5
NameN-{(1S,2R)-1-(3,5-DIFLUOROBENZYL)-2-HYDROXY-2-[(2R,4R)-4-PHENOXYPYRROLIDIN-2-YL]ETHYL}-3-{[(2R)-2-(METHOXYMETHYL)PYRROLIDIN-1-YL]CARBONYL}-5-METHYLBENZAMIDE
ChEMBLCHEMBL403195
DrugBank
ZINCZINC000014209296
PDB chain2qmg 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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PDB2qmg Discovery of an orally efficaceous 4-phenoxypyrrolidine-based BACE-1 inhibitor.
Resolution1.89 Å
Binding residue
(original residue number in PDB)		G72 L91 D93 G95 Y132 T133 Q134 F169 I171 R189 D289 G291 T292 T293 R296
Binding residue
(residue number reindexed from 1)		G15 L34 D36 G38 Y75 T76 Q77 F112 I114 R132 D232 G234 T235 T236 R239
Annotation score1
Binding affinityMOAD: Ki=0.7nM
PDBbind-CN: -logKd/Ki=9.15,Ki=0.7nM
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:2qmg, PDBe:2qmg, PDBj:2qmg
PDBsum2qmg
PubMed17980584
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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