Structure of PDB 5rfa Chain A Binding Site BS01

Receptor Information
>5rfa Chain A (length=301) 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
S
Ligand information
Ligand IDJGY
InChIInChI=1S/C10H15N3O2/c1-13-5-4-9(12-13)10(14)11-7-8-3-2-6-15-8/h4-5,8H,2-3,6-7H2,1H3,(H,11,14)/t8-/m0/s1
InChIKeyWBAZBPMBDLSPCX-QMMMGPOBSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.6Cn1ccc(n1)C(=O)NCC2CCCO2
CACTVS 3.385Cn1ccc(n1)C(=O)NC[CH]2CCCO2
CACTVS 3.385
OpenEye OEToolkits 2.0.6		Cn1ccc(n1)C(=O)NC[C@@H]2CCCO2
ACDLabs 12.01C(C1CCCO1)NC(c2ccn(C)n2)=O
FormulaC10 H15 N3 O2
Name1-methyl-N-{[(2S)-oxolan-2-yl]methyl}-1H-pyrazole-3-carboxamide
ChEMBLCHEMBL4975751
DrugBank
ZINCZINC000001001271
PDB chain5rfa Chain A Residue 403 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5rfa Crystallographic and electrophilic fragment screening of the SARS-CoV-2 main protease.
Resolution1.52 Å
Binding residue
(original residue number in PDB)		M6 F8 Q127 R298 Q299
Binding residue
(residue number reindexed from 1)		M6 F8 Q127 R298 Q299
Annotation score1
Binding affinityBindingDB: IC50=99000nM
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:5rfa, PDBe:5rfa, PDBj:5rfa
PDBsum5rfa
PubMed33028810
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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