Structure of PDB 7d7l Chain A Binding Site BS03

Receptor Information
>7d7l Chain A (length=312) 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]
TIKVFTTVDNINLHTQVVDMSMTYGQQFGPTYLDGADVTKIKPHNSHEGK
TFYVLPNDDTLRVEAFEYYHTTDPSFLGRYMSALNHTKKWKYPQVNGLTS
IKWADNNSYLATALLTLQQIELKFNPPALQDAYYRARAGEAANFCALILA
YCNKTVGELGDVRETMSYLFQHANLDSCKRVLNVVCKTCGQQQTTLKGVE
AVMYMGTLSYEQFKKGVQIPCTCGKQATKYLVQQESPFVMMSAPPAQYEL
KHGTFTCASEYTGNYQCGHYKHITSKETLYCIDGALLTKSSEYKGPITDV
FYKENSYTTTIK
Ligand information
Ligand IDGXU
InChIInChI=1S/C20H19N4O3/c1-13-23(9-10-27-2)17-18(24(13)12-14-11-21-7-8-22-14)20(26)16-6-4-3-5-15(16)19(17)25/h3-8,11H,9-10,12H2,1-2H3/q+1
InChIKeyOTSOOHRUMBRSHZ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7Cc1n(c2c([n+]1Cc3cnccn3)C(=O)c4ccccc4C2=O)CCOC
CACTVS 3.385COCCn1c(C)[n+](Cc2cnccn2)c3C(=O)c4ccccc4C(=O)c13
FormulaC20 H19 N4 O3
Name1-(2-methoxyethyl)-2-methyl-3-(pyrazin-2-ylmethyl)benzo[f]benzimidazol-3-ium-4,9-dione
ChEMBLCHEMBL2110734
DrugBankDB17062
ZINCZINC000001908550
PDB chain7d7l 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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PDB7d7l High-throughput screening identifies established drugs as SARS-CoV-2 PLpro inhibitors.
Resolution2.11 Å
Binding residue
(original residue number in PDB)		P247 P248 Y264 Y268 Y273 T301
Binding residue
(residue number reindexed from 1)		P244 P245 Y261 Y265 Y270 T298
Annotation score1
Binding affinityBindingDB: IC50=13600nM
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:0008234 cysteine-type peptidase activity
Biological Process
GO:0006508 proteolysis

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Molecular Function
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Biological Process
External links
PDB RCSB:7d7l, PDBe:7d7l, PDBj:7d7l
PDBsum7d7l
PubMed33864621
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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