Structure of PDB 7dpv Chain B Binding Site BS01

Receptor Information
>7dpv Chain B (length=299) 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]
GFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLN
PNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKY
KFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFN
IDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTIT
VNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILG
PLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
Ligand information
Ligand IDHF0
InChIInChI=1S/C16H14O8/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/h2-5,15-20,22H,1H3/t15-,16+/m1/s1
InChIKeyOEYMPTGVGRACKD-CVEARBPZSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 2.0.7COc1cc(c2c(c1)O[C@H]([C@@H](C2=O)O)c3cc(c(c(c3)O)O)O)O
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@@H](O)[C@@H](Oc2c1)c3cc(O)c(O)c(O)c3
CACTVS 3.385COc1cc(O)c2C(=O)[CH](O)[CH](Oc2c1)c3cc(O)c(O)c(O)c3
FormulaC16 H14 O8
Name(2S,3S)-3,5-dihydroxy-7-methoxy-2-(3,4,5-trihydroxyphenyl)chroman-4-one
ChEMBL
DrugBank
ZINC
PDB chain7dpv Chain B Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7dpv Identification of pyrogallol as a warhead in design of covalent inhibitors for the SARS-CoV-2 3CL protease.
Resolution2.35 Å
Binding residue
(original residue number in PDB)		H41 G143 C145 M165 D187 R188 Q189
Binding residue
(residue number reindexed from 1)		H40 G142 C144 M164 D186 R187 Q188
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
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Biological Process
External links
PDB RCSB:7dpv, PDBe:7dpv, PDBj:7dpv
PDBsum7dpv
PubMed34131140
UniProtP0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)

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