Structure of PDB 7m8z Chain A Binding Site BS01

Receptor Information
>7m8z Chain A (length=297) 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]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTMLNPN
YEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKF
VRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNID
DCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNV
LAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLS
AQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS
Ligand information
Ligand IDYTV
InChIInChI=1S/C25H23ClN4O5/c1-25(2,34)5-7-35-19-9-15(8-17(26)11-19)20-10-16(21-13-28-24(33)29-22(21)31)14-30(23(20)32)18-4-3-6-27-12-18/h3-4,6,8-14,34H,5,7H2,1-2H3,(H2,28,29,31,33)
InChIKeyJKRQOBZCXCNDAL-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.385CC(C)(O)CCOc1cc(Cl)cc(c1)C2=CC(=CN(C2=O)c3cccnc3)C4=CNC(=O)NC4=O
OpenEye OEToolkits 2.0.7CC(C)(CCOc1cc(cc(c1)Cl)C2=CC(=CN(C2=O)c3cccnc3)C4=CNC(=O)NC4=O)O
ACDLabs 12.01CC(C)(O)CCOc1cc(cc(Cl)c1)C1=CC(=CN(c2cnccc2)C1=O)C1=CNC(=O)NC1=O
FormulaC25 H23 Cl N4 O5
Name5-{3-[3-chloro-5-(3-hydroxy-3-methylbutoxy)phenyl]-2-oxo-2H-[1,3'-bipyridin]-5-yl}pyrimidine-2,4(1H,3H)-dione
ChEMBL
DrugBank
ZINC
PDB chain7m8z 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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PDB7m8z Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease.
Resolution1.79 Å
Binding residue
(original residue number in PDB)
T25 H41 F140 L141 N142 G143 C145 H163 M165 E166 D187 R188 Q189 T190 Q192
Binding residue
(residue number reindexed from 1)
T25 H41 F137 L138 N139 G140 C142 H159 M161 E162 D183 R184 Q185 T186 Q188
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:7m8z, PDBe:7m8z, PDBj:7m8z
PDBsum7m8z
PubMed34161756
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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