Structure of PDB 7gh8 Chain A Binding Site BS01

Receptor Information

>7gh8 Chain A (length=304) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT

Ligand information

• Ligand ID: Q3U
• InChI: InChI=1S/C12H11ClN4O/c13-8-2-1-3-10(4-8)16-12(18)17-11-5-9(14)6-15-7-11/h1-7H,14H2,(H2,16,17,18)
• InChIKey: NNDMILIBNSMJII-UHFFFAOYSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1cc(cc(c1)Cl)NC(=O)Nc2cc(cnc2)N
  CACTVS 3.385: Nc1cncc(NC(=O)Nc2cccc(Cl)c2)c1
  ACDLabs 12.01: O=C(Nc1cc(N)cnc1)Nc1cccc(Cl)c1
• Formula: C12 H11 Cl N4 O
• Name: N-(5-aminopyridin-3-yl)-N'-(3-chlorophenyl)urea
• PDB chain: 7gh8 Chain A Residue 1001

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7gh8 Open science discovery of potent noncovalent SARS-CoV-2 main protease inhibitors
• Resolution: 1.52 Å
• Binding residue (original residue number in PDB): H41 M49 F140 L141 C145 H163 M165 E166 D187 R188
• Binding residue (residue number reindexed from 1): H41 M49 F140 L141 C145 H163 M165 E166 D187 R188
• Annotation score: 1

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

External links

• PDB: RCSB:7gh8, PDBe:7gh8, PDBj:7gh8
• PDBsum: 7gh8
• PubMed: 37943932
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)