Structure of PDB 7m91 Chain A Binding Site BS01

Receptor Information
>7m91 Chain A (length=303) 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]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCSG
VTF
Ligand information
Ligand IDYU4
InChIInChI=1S/C23H16ClF3N4O4/c24-15-6-13(7-17(9-15)35-5-3-23(25,26)27)18-8-14(19-11-29-22(34)30-20(19)32)12-31(21(18)33)16-2-1-4-28-10-16/h1-2,4,6-12H,3,5H2,(H2,29,30,32,34)
InChIKeyBHQBUUBHCKLKLD-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385FC(F)(F)CCOc1cc(Cl)cc(c1)C2=CC(=CN(C2=O)c3cccnc3)C4=CNC(=O)NC4=O
ACDLabs 12.01FC(F)(F)CCOc1cc(cc(Cl)c1)C1=CC(=CN(c2cnccc2)C1=O)C1=CNC(=O)NC1=O
OpenEye OEToolkits 2.0.7c1cc(cnc1)N2C=C(C=C(C2=O)c3cc(cc(c3)Cl)OCCC(F)(F)F)C4=CNC(=O)NC4=O
FormulaC23 H16 Cl F3 N4 O4
Name5-{3-[3-chloro-5-(3,3,3-trifluoropropoxy)phenyl]-2-oxo-2H-[1,3'-bipyridin]-5-yl}pyrimidine-2,4(1H,3H)-dione
ChEMBLCHEMBL4863054
DrugBank
ZINC
PDB chain7m91 Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB7m91 Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease.
Resolution1.95 Å
Binding residue
(original residue number in PDB)		T25 H41 F140 L141 N142 G143 C145 H163 M165 E166 D187 Q189 Q192
Binding residue
(residue number reindexed from 1)		T25 H41 F138 L139 N140 G141 C143 H161 M163 E164 D185 Q187 Q190
Annotation score1
Binding affinityBindingDB: IC50=25nM,EC50=820nM
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:7m91, PDBe:7m91, PDBj:7m91
PDBsum7m91
PubMed34161756
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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