Structure of PDB 7m8y Chain A Binding Site BS01

Receptor Information
>7m8y Chain A (length=305) 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
NIDYDCVSFCYMHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTIT
VNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILG
PLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS
GVTFQ
Ligand information
Ligand IDYTM
InChIInChI=1S/C28H21ClN4O4/c29-21-11-19(12-23(14-21)37-10-8-18-5-2-1-3-6-18)24-13-20(25-16-31-28(36)32-26(25)34)17-33(27(24)35)22-7-4-9-30-15-22/h1-7,9,11-17H,8,10H2,(H2,31,32,34,36)
InChIKeyJVSFPWJWCIUVJO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7c1ccc(cc1)CCOc2cc(cc(c2)Cl)C3=CC(=CN(C3=O)c4cccnc4)C5=CNC(=O)NC5=O
ACDLabs 12.01O=C1NC=C(C2=CN(c3cnccc3)C(=O)C(=C2)c2cc(OCCc3ccccc3)cc(Cl)c2)C(=O)N1
CACTVS 3.385Clc1cc(OCCc2ccccc2)cc(c1)C3=CC(=CN(C3=O)c4cccnc4)C5=CNC(=O)NC5=O
FormulaC28 H21 Cl N4 O4
Name5-{3-[3-chloro-5-(2-phenylethoxy)phenyl]-2-oxo-2H-[1,3'-bipyridin]-5-yl}pyrimidine-2,4(1H,3H)-dione
ChEMBL
DrugBank
ZINC
PDB chain7m8y 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

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB7m8y Structure-guided design of a perampanel-derived pharmacophore targeting the SARS-CoV-2 main protease.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		T25 H41 M49 F140 L141 N142 G143 C145 M165 E166 P168 D187 R188 Q189 T190
Binding residue
(residue number reindexed from 1)		T25 H41 M49 F140 L141 N142 G143 C145 M164 E165 P167 D186 R187 Q188 T189
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
View graph for
Biological Process
External links
PDB RCSB:7m8y, PDBe:7m8y, PDBj:7m8y
PDBsum7m8y
PubMed34161756
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]