Structure of PDB 5srh Chain A Binding Site BS02

Receptor Information

>5srh Chain A (length=167) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: R9F
• InChI: InChI=1S/C10H7FN4/c11-5-1-2-6-7(3-5)15-10-8(6)9(12)13-4-14-10/h1-4H,(H3,12,13,14,15)
• InChIKey: LFMLBPCSGKLSSW-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: Nc1ncnc2[nH]c3cc(F)ccc3c12
  ACDLabs 12.01: Fc1ccc2c(c1)[NH]c1ncnc(N)c21
  OpenEye OEToolkits 2.0.7: c1cc2c(cc1F)[nH]c3c2c(ncn3)N
• Formula: C10 H7 F N4
• Name: 7-fluoro-9H-pyrimido[4,5-b]indol-4-amine
• PDB chain: 5srh Chain A Residue 303

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5srh Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
• Resolution: 1.05 Å
• Binding residue (original residue number in PDB): I23 G48 V49 A52 A154 F156
• Binding residue (residue number reindexed from 1): I21 G46 V47 A50 A152 F154
• 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.-

External links

• PDB: RCSB:5srh, PDBe:5srh, PDBj:5srh
• PDBsum: 5srh
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)