Structure of PDB 3zmg Chain A Binding Site BS01

Receptor Information
>3zmg Chain A (length=385) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RGSFVEMVDNLRGKSGQGYYVEMTVGSPPQTLNILVDTGSSNFAVGAAPH
PFLHRYYQRQLSSTYRDLRKGVYVPYTQGKWEGELGTDLVSIPHGPNVTV
RANIAAITESDKFFINGSNWEGILGLAYAEIARPDDSLEPFFDSLVKQTH
VPNLFSLQLCGAGFPLASVGGSMIIGGIDHSLYTGSLWYTPIRREWYYEV
IIVRVEINGQDLKMDCKEYNYDKSIVDSGTTNLRLPKKVFEAAVASIKAA
SSTEKFPDGFWLGEQLVCWQAGTTPWNIFPVISLYLMGEVTNQSFRITIL
PQQYLRPVEDVATSQDDCYKFAISQSSTGTVMGAVIMEGFYVVFDRARKR
IGFAVSACHVHDEFRTAAVEGPFVTLDMEDCGYNI
Ligand information
Ligand ID6Z0
InChIInChI=1S/C18H14F3N5O2/c1-17(18(20,21)9-28-16(23)26-17)12-6-11(3-4-13(12)19)25-15(27)14-5-2-10(7-22)8-24-14/h2-6,8H,9H2,1H3,(H2,23,26)(H,25,27)/t17-/m1/s1
InChIKeyDVMUZHLUMHPCGZ-QGZVFWFLSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2[H]/N=C\1/N[C@](C(CO1)(F)F)(C)c2cc(ccc2F)NC(=O)c3ccc(cn3)C#N
OpenEye OEToolkits 1.9.2CC1(C(COC(=N)N1)(F)F)c2cc(ccc2F)NC(=O)c3ccc(cn3)C#N
ACDLabs 12.01FC1(F)C(NC(=[N@H])OC1)(c3cc(NC(=O)c2ncc(C#N)cc2)ccc3F)C
CACTVS 3.385C[C]1(NC(=N)OCC1(F)F)c2cc(NC(=O)c3ccc(cn3)C#N)ccc2F
CACTVS 3.385C[C@@]1(NC(=N)OCC1(F)F)c2cc(NC(=O)c3ccc(cn3)C#N)ccc2F
FormulaC18 H14 F3 N5 O2
NameN-[3-[(4R)-2-azanylidene-5,5-bis(fluoranyl)-4-methyl-1,3-oxazinan-4-yl]-4-fluoranyl-phenyl]-5-cyano-pyridine-2-carboxamide
ChEMBLCHEMBL2347215
DrugBank
ZINCZINC000095602954
PDB chain3zmg Chain A Residue 1448 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3zmg Beta-Secretase (Bace1) Inhibitors with High in Vivo Efficacy Suitable for Clinical Evaluation in Alzheimer'S Disease.
Resolution1.74 Å
Binding residue
(original residue number in PDB)		G72 Q73 G74 L91 D93 Y132 F169 D289 G291 T293
Binding residue
(residue number reindexed from 1)		G16 Q17 G18 L35 D37 Y76 F113 D227 G229 T231
Annotation score1
Binding affinityMOAD: ic50=0.023uM
PDBbind-CN: -logKd/Ki=7.64,IC50=23nM
Enzymatic activity
Catalytic site (original residue number in PDB) D93 S96 N98 A100 Y132 D289 T292
Catalytic site (residue number reindexed from 1) D37 S40 N42 A44 Y76 D227 T230
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:3zmg, PDBe:3zmg, PDBj:3zmg
PDBsum3zmg
PubMed23590342
UniProtP56817|BACE1_HUMAN Beta-secretase 1 (Gene Name=BACE1)

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