Structure of PDB 5rgx Chain A Binding Site BS01

Receptor Information
>5rgx 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 IDUGP
InChIInChI=1S/C15H13N3O/c1-11-5-6-17-10-14(11)18-15(19)8-12-3-2-4-13(7-12)9-16/h2-7,10H,8H2,1H3,(H,18,19)
InChIKeyOTFRLGRHXMKEAF-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385
OpenEye OEToolkits 2.0.7		Cc1ccncc1NC(=O)Cc2cccc(c2)C#N
ACDLabs 12.01N(C(Cc1cccc(C#N)c1)=O)c2cnccc2C
FormulaC15 H13 N3 O
Name2-(3-cyanophenyl)-N-(4-methylpyridin-3-yl)acetamide
ChEMBL
DrugBank
ZINC
PDB chain5rgx 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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PDB5rgx PanDDA analysis group deposition SARS-CoV-2 main protease fragment screen
Resolution1.69 Å
Binding residue
(original residue number in PDB)		H41 M49 F140 L141 H163 H164 M165 E166 D187 R188 Q189
Binding residue
(residue number reindexed from 1)		H41 M49 F140 L141 H163 H164 M165 E166 D187 R188 Q189
Annotation score1
Binding affinityBindingDB: IC50=43800nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:5rgx, PDBe:5rgx, PDBj:5rgx
PDBsum5rgx
PubMed
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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