Structure of PDB 5rgi Chain A Binding Site BS01

Receptor Information
>5rgi 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 IDU0P
InChIInChI=1S/C10H15N3O2/c1-7-5-9(12-15-7)6-13(2)10(14)11-8-3-4-8/h5,8H,3-4,6H2,1-2H3,(H,11,14)
InChIKeyQKUCRJSBLDVNFL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CN(Cc1cc(C)on1)C(=O)NC2CC2
OpenEye OEToolkits 2.0.7Cc1cc(no1)CN(C)C(=O)NC2CC2
ACDLabs 12.01C(N(C)Cc1noc(c1)C)(NC2CC2)=O
FormulaC10 H15 N3 O2
NameN'-cyclopropyl-N-methyl-N-[(5-methyl-1,2-oxazol-3-yl)methyl]urea
ChEMBL
DrugBank
ZINCZINC000046885388
PDB chain5rgi Chain A Residue 404 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5rgi Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.
Resolution1.57 Å
Binding residue
(original residue number in PDB)		F140 L141 N142 G143 C145 H163 H164 E166
Binding residue
(residue number reindexed from 1)		F140 L141 N142 G143 C145 H163 H164 E166
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:5rgi, PDBe:5rgi, PDBj:5rgi
PDBsum5rgi
PubMed33028810
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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