Structure of PDB 6m2n Chain C Binding Site BS01

Receptor Information
>6m2n Chain C (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
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF
Ligand information
Ligand ID3WL
InChIInChI=1S/C15H10O5/c16-9-6-11(8-4-2-1-3-5-8)20-12-7-10(17)14(18)15(19)13(9)12/h1-7,17-19H
InChIKeyFXNFHKRTJBSTCS-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.9.2c1ccc(cc1)C2=CC(=O)c3c(cc(c(c3O)O)O)O2
CACTVS 3.385Oc1cc2OC(=CC(=O)c2c(O)c1O)c3ccccc3
ACDLabs 12.01O=C1c3c(O)c(O)c(O)cc3OC(=C1)c2ccccc2
FormulaC15 H10 O5
Name5,6,7-trihydroxy-2-phenyl-4H-chromen-4-one;
Baicalein
ChEMBLCHEMBL8260
DrugBankDB16101
ZINCZINC000003871633
PDB chain6m2n Chain C Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6m2n Anti-SARS-CoV-2 activities in vitro of Shuanghuanglian preparations and bioactive ingredients.
Resolution2.198 Å
Binding residue
(original residue number in PDB)		H41 M49 N142 G143 C145 M165
Binding residue
(residue number reindexed from 1)		H41 M49 N142 G143 C145 M165
Annotation score1
Binding affinityMOAD: Kd=4.03uM
BindingDB: IC50=20nM,EC50=2940nM
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

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Molecular Function
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Biological Process
External links
PDB RCSB:6m2n, PDBe:6m2n, PDBj:6m2n
PDBsum6m2n
PubMed32737471
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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