Structure of PDB 5ygy Chain A Binding Site BS01

Receptor Information
>5ygy Chain A (length=381) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
GRRGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAA
PHPFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNV
TVRANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQ
THVPNLFSLQLCGASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIV
RVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASST
EKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQ
YLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGF
AVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID0B6
InChIInChI=1S/C19H15F2N5O2/c1-19(7-13(8-20)28-18(23)26-19)14-6-12(3-4-15(14)21)25-17(27)16-5-2-11(9-22)10-24-16/h2-7,10H,8H2,1H3,(H2,23,26)(H,25,27)/t19-/m0/s1
InChIKeyORHZQSYKGHHDOP-IBGZPJMESA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6C[C@]1(C=C(OC(=N1)N)CF)c2cc(ccc2F)NC(=O)c3ccc(cn3)C#N
CACTVS 3.385C[C]1(C=C(CF)OC(=N1)N)c2cc(NC(=O)c3ccc(cn3)C#N)ccc2F
CACTVS 3.385C[C@]1(C=C(CF)OC(=N1)N)c2cc(NC(=O)c3ccc(cn3)C#N)ccc2F
OpenEye OEToolkits 2.0.6CC1(C=C(OC(=N1)N)CF)c2cc(ccc2F)NC(=O)c3ccc(cn3)C#N
FormulaC19 H15 F2 N5 O2
Name~{N}-[3-[(4~{S})-2-azanyl-6-(fluoranylmethyl)-4-methyl-1,3-oxazin-4-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide
ChEMBLCHEMBL4213486
DrugBank
ZINC
PDB chain5ygy Chain A Residue 509 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5ygy Rational Design of Novel 1,3-Oxazine Based beta-Secretase (BACE1) Inhibitors: Incorporation of a Double Bond To Reduce P-gp Efflux Leading to Robust A beta Reduction in the Brain
Resolution2.3 Å
Binding residue
(original residue number in PDB)		G11 Q12 G13 L30 D32 Y71 F108 D228 G230 T232
Binding residue
(residue number reindexed from 1)		G18 Q19 G20 L37 D39 Y78 F115 D224 G226 T228
Annotation score1
Binding affinityMOAD: ic50=59nM
BindingDB: IC50=3.6nM
Enzymatic activity
Catalytic site (original residue number in PDB) D32 S35 N37 A39 Y71 D228 T231
Catalytic site (residue number reindexed from 1) D39 S42 N44 A46 Y78 D224 T227
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:5ygy, PDBe:5ygy, PDBj:5ygy
PDBsum5ygy
PubMed29733614
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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