Structure of PDB 6bfx Chain A Binding Site BS01

Receptor Information
>6bfx Chain A (length=389) 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
RARKRIGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand IDDKJ
InChIInChI=1S/C21H32F2N2O4/c1-12-20(29-11-21(3,4)5)28-10-18(24-12)19(27)17(25-13(2)26)8-14-6-15(22)9-16(23)7-14/h6-7,9,12,17-20,24,27H,8,10-11H2,1-5H3,(H,25,26)/t12-,17-,18+,19-,20-/m0/s1
InChIKeyMTSIVXGKWLWPKB-VVEMMYRFSA-N
SMILES
SoftwareSMILES
CACTVS 3.385C[CH]1N[CH](CO[CH]1OCC(C)(C)C)[CH](O)[CH](Cc2cc(F)cc(F)c2)NC(C)=O
OpenEye OEToolkits 2.0.6CC1C(OCC(N1)C(C(Cc2cc(cc(c2)F)F)NC(=O)C)O)OCC(C)(C)C
OpenEye OEToolkits 2.0.6C[C@H]1[C@@H](OC[C@@H](N1)[C@H]([C@H](Cc2cc(cc(c2)F)F)NC(=O)C)O)OCC(C)(C)C
CACTVS 3.385C[C@@H]1N[C@H](CO[C@H]1OCC(C)(C)C)[C@@H](O)[C@H](Cc2cc(F)cc(F)c2)NC(C)=O
ACDLabs 12.01O=C(C)NC(Cc1cc(cc(c1)F)F)C(C2NC(C)C(OC2)OCC(C)(C)C)O
FormulaC21 H32 F2 N2 O4
NameN-{(1S,2S)-3-(3,5-difluorophenyl)-1-[(3R,5S,6R)-6-(2,2-dimethylpropoxy)-5-methylmorpholin-3-yl]-1-hydroxypropan-2-yl}acetamide
ChEMBLCHEMBL4116547
DrugBank
ZINCZINC000038216060
PDB chain6bfx Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6bfx Optimization of Hydroxyethylamine Transition State Isosteres as Aspartic Protease Inhibitors by Exploiting Conformational Preferences.
Resolution1.99 Å
Binding residue
(original residue number in PDB)		D32 G34 S35 Y71 T72 F108 Y198 D228 G230
Binding residue
(residue number reindexed from 1)		D36 G38 S39 Y75 T76 F112 Y202 D232 G234
Annotation score1
Binding affinityMOAD: ic50=0.079uM
PDBbind-CN: -logKd/Ki=7.10,IC50=0.079uM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
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:6bfx, PDBe:6bfx, PDBj:6bfx
PDBsum6bfx
PubMed29088532
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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