Structure of PDB 7dpu Chain B Binding Site BS01

Receptor Information
>7dpu Chain B (length=306) 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
SGVTFQ
Ligand information
Ligand IDHER
InChIInChI=1S/C16H12O8/c1-23-7-4-8(17)12-11(5-7)24-16(15(22)14(12)21)6-2-9(18)13(20)10(19)3-6/h2-5,17-20,22H,1H3
InChIKeyBDZXSHDKBKYQKJ-UHFFFAOYSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7COc1cc(c2c(c1)OC(=C(C2=O)O)c3cc(c(c(c3)O)O)O)O
CACTVS 3.385COc1cc(O)c2C(=O)C(=C(Oc2c1)c3cc(O)c(O)c(O)c3)O
FormulaC16 H12 O8
Name7-methoxy-3,5-bis(oxidanyl)-2-[3,4,5-tris(oxidanyl)phenyl]chromen-4-one
ChEMBLCHEMBL5288812
DrugBank
ZINC
PDB chain7dpu Chain B 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]
PDB7dpu Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease.
Resolution1.75 Å
Binding residue
(original residue number in PDB)		H41 M49 G143 C145 M165 E166 D187 R188
Binding residue
(residue number reindexed from 1)		H41 M49 G143 C145 M165 E166 D187 R188
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:7dpu, PDBe:7dpu, PDBj:7dpu
PDBsum7dpu
PubMed34131140
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

[Back to BioLiP]