Structure of PDB 5rgy Chain A Binding Site BS01

Receptor Information
>5rgy Chain A (length=304) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT
Ligand information
Ligand IDUGS
InChIInChI=1S/C18H16N2O2/c1-22-16-8-9-19-17(12-16)20-18(21)11-13-6-7-14-4-2-3-5-15(14)10-13/h2-10,12H,11H2,1H3,(H,19,20,21)
InChIKeyLGUXBXKDCLNCEH-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01N(C(=O)Cc2cc1c(cccc1)cc2)c3cc(ccn3)OC
OpenEye OEToolkits 2.0.7COc1ccnc(c1)NC(=O)Cc2ccc3ccccc3c2
CACTVS 3.385COc1ccnc(NC(=O)Cc2ccc3ccccc3c2)c1
FormulaC18 H16 N2 O2
NameN-(4-methoxypyridin-2-yl)-2-(naphthalen-2-yl)acetamide
ChEMBLCHEMBL4744511
DrugBank
ZINC
PDB chain5rgy Chain A Residue 1001 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5rgy PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen
Resolution1.976 Å
Binding residue
(original residue number in PDB)		M49 H164 M165 E166 P168 Q189 T190
Binding residue
(residue number reindexed from 1)		M49 H164 M165 E166 P168 Q189 T190
Annotation score1
Enzymatic activity
Enzyme Commision number 2.1.1.56: mRNA (guanine-N(7))-methyltransferase.
2.1.1.57: methyltransferase cap1.
2.7.7.48: RNA-directed RNA polymerase.
2.7.7.50: mRNA guanylyltransferase.
3.1.13.-
3.4.19.12: ubiquitinyl hydrolase 1.
3.4.22.-
3.4.22.69: SARS coronavirus main proteinase.
3.6.4.12: DNA helicase.
3.6.4.13: RNA helicase.
4.6.1.-
Gene Ontology
Molecular Function
GO:0008233 peptidase activity
Biological Process
GO:0019082 viral protein processing

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:5rgy, PDBe:5rgy, PDBj:5rgy
PDBsum5rgy
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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