Structure of PDB 7m8m Chain A Binding Site BS01

Receptor Information
>7m8m 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 IDYSG
InChIInChI=1S/C23H19ClN4O4/c1-2-6-32-18-8-14(7-16(24)10-18)19-9-15(20-12-26-23(31)27-21(20)29)13-28(22(19)30)17-4-3-5-25-11-17/h3-5,7-13H,2,6H2,1H3,(H2,26,27,29,31)
InChIKeyGJCBTWHGKCNYAB-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 12.01O=C1NC=C(C2=CN(c3cnccc3)C(=O)C(=C2)c2cc(OCCC)cc(Cl)c2)C(=O)N1
CACTVS 3.385CCCOc1cc(Cl)cc(c1)C2=CC(=CN(C2=O)c3cccnc3)C4=CNC(=O)NC4=O
OpenEye OEToolkits 2.0.7CCCOc1cc(cc(c1)Cl)C2=CC(=CN(C2=O)c3cccnc3)C4=CNC(=O)NC4=O
FormulaC23 H19 Cl N4 O4
Name5-[3-(3-chloro-5-propoxyphenyl)-2-oxo-2H-[1,3'-bipyridin]-5-yl]pyrimidine-2,4(1H,3H)-dione
ChEMBLCHEMBL4872194
DrugBank
ZINC
PDB chain7m8m 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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PDB7m8m Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease.
Resolution1.78 Å
Binding residue
(original residue number in PDB)		T25 T26 H41 M49 F140 L141 N142 G143 C145 H163 M165 E166 D187 R188
Binding residue
(residue number reindexed from 1)		T25 T26 H41 M49 F140 L141 N142 G143 C145 H163 M165 E166 D187 R188
Annotation score1
Binding affinityBindingDB: IC50=120nM
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
View graph for
Biological Process
External links
PDB RCSB:7m8m, PDBe:7m8m, PDBj:7m8m
PDBsum7m8m
PubMed34161756
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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