Structure of PDB 7gs5 Chain B Binding Site BS01

Receptor Information

>7gs5 Chain B (length=304) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT

Ligand information

• Ligand ID: 0TI
• InChI: InChI=1S/C8H6FNO2/c9-4-1-2-6-5(3-4)7(11)8(12)10-6/h1-3,7,11H,(H,10,12)/t7-/m1/s1
• InChIKey: XYDTZHMQTYEJQN-SSDOTTSWSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: c1cc2c(cc1F)C(C(=O)N2)O
  CACTVS 3.385: O[C@H]1C(=O)Nc2ccc(F)cc12
  OpenEye OEToolkits 1.7.6: c1cc2c(cc1F)[C@H](C(=O)N2)O
  CACTVS 3.385: O[CH]1C(=O)Nc2ccc(F)cc12
  ACDLabs 12.01: c2cc1NC(=O)C(O)c1cc2F
• Formula: C8 H6 F N O2
• Name: (3R)-5-fluoro-3-hydroxy-1,3-dihydro-2H-indol-2-one
• ZINC: ZINC000100380560
• PDB chain: 7gs5 Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7gs5 Fragment-based screening targeting an open form of the SARS-CoV-2 main protease binding pocket.
• Resolution: 1.88 Å
• Binding residue (original residue number in PDB): H41 G143 C145
• Binding residue (residue number reindexed from 1): H41 G143 C145
• 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:7gs5, PDBe:7gs5, PDBj:7gs5
• PDBsum: 7gs5
• PubMed: 38289714
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)