Structure of PDB 7dpp Chain A Binding Site BS01

Receptor Information
>7dpp Chain A (length=294) 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]
SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICPNYEDL
LIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRIQ
PGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDCV
SFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLAW
LYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQT
GIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS
Ligand information
Ligand IDMYC
InChIInChI=1S/C15H10O8/c16-6-3-7(17)11-10(4-6)23-15(14(22)13(11)21)5-1-8(18)12(20)9(19)2-5/h1-4,16-20,22H
InChIKeyIKMDFBPHZNJCSN-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04O=C1c3c(OC(=C1O)c2cc(O)c(O)c(O)c2)cc(O)cc3O
OpenEye OEToolkits 1.5.0c1c(cc(c(c1O)O)O)C2=C(C(=O)c3c(cc(cc3O2)O)O)O
CACTVS 3.341Oc1cc(O)c2C(=O)C(=C(Oc2c1)c3cc(O)c(O)c(O)c3)O
FormulaC15 H10 O8
Name3,5,7-TRIHYDROXY-2-(3,4,5-TRIHYDROXYPHENYL)-4H-CHROMEN-4-ONE;
2-(3,4,5-TRIHYDROXYPHENYL)-3,5,7-TRIHYDROXY-4H-1-BENZOPYRAN-4-ONE;
3,3',4',5,5',7-HEXAHYDROXYFLAVONE;
MYRICETIN;
CANNABISCETIN
ChEMBLCHEMBL164
DrugBankDB02375
ZINCZINC000003874317
PDB chain7dpp Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7dpp Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease.
Resolution2.1 Å
Binding residue
(original residue number in PDB)		H41 G143 C145 H164 D187
Binding residue
(residue number reindexed from 1)		H41 G136 C138 H157 D180
Annotation score1
Binding affinityBindingDB: IC50=220nM
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:7dpp, PDBe:7dpp, PDBj:7dpp
PDBsum7dpp
PubMed34131140
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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