Structure of PDB 5ygx Chain A Binding Site BS01

Receptor Information
>5ygx 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]
GSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPHP
FLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTVR
ANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTHV
PNLFSLQLCGAVLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEVIIV
RVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVKSIKAASST
EKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITILPQQ
YLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKRIGF
AVSACHVHDEFRTAAVEGPFVTLDMEDCGYN
Ligand information
Ligand ID0B5
InChIInChI=1S/C19H18F5N5O3/c1-18(14(22)15(19(2,23)24)32-17(25)29-18)10-5-9(3-4-11(10)21)28-16(30)12-6-27-13(7-26-12)31-8-20/h3-7,14-15H,8H2,1-2H3,(H2,25,29)(H,28,30)/t14-,15-,18+/m0/s1
InChIKeyDKIWJWSKVCKJPV-RLFYNMQTSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6CC1(C(C(OC(=N1)N)C(C)(F)F)F)c2cc(ccc2F)NC(=O)c3cnc(cn3)OCF
CACTVS 3.385CC(F)(F)[C@H]1OC(=N[C@@](C)([C@H]1F)c2cc(NC(=O)c3cnc(OCF)cn3)ccc2F)N
OpenEye OEToolkits 2.0.6C[C@]1([C@H]([C@H](OC(=N1)N)C(C)(F)F)F)c2cc(ccc2F)NC(=O)c3cnc(cn3)OCF
CACTVS 3.385CC(F)(F)[CH]1OC(=N[C](C)([CH]1F)c2cc(NC(=O)c3cnc(OCF)cn3)ccc2F)N
FormulaC19 H18 F5 N5 O3
Name~{N}-[3-[(4~{R},5~{R},6~{S})-2-azanyl-6-[1,1-bis(fluoranyl)ethyl]-5-fluoranyl-4-methyl-5,6-dihydro-1,3-oxazin-4-yl]-4-fluoranyl-phenyl]-5-(fluoranylmethoxy)pyrazine-2-carboxamide
ChEMBLCHEMBL4226994
DrugBank
ZINC
PDB chain5ygx 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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PDB5ygx Discovery of Potent and Centrally Active 6-Substituted 5-Fluoro-1,3-dihydro-oxazine beta-Secretase (BACE1) Inhibitors via Active Conformation Stabilization
Resolution2.2 Å
Binding residue
(original residue number in PDB)		G11 Q12 G13 L30 D32 Y71 F108 I118 D228 G230 T232 A335
Binding residue
(residue number reindexed from 1)		G15 Q16 G17 L34 D36 Y75 F112 I122 D224 G226 T228 A331
Annotation score1
Binding affinityMOAD: ic50=8.74nM
BindingDB: IC50=8.7nM
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 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:5ygx, PDBe:5ygx, PDBj:5ygx
PDBsum5ygx
PubMed29775538
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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