Structure of PDB 5s3q Chain A Binding Site BS02

Receptor Information

>5s3q Chain A (length=164) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALN
KATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGE
DIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLA
VFDKNLYDKLVSSF

Ligand information

• Ligand ID: W2A
• InChI: InChI=1S/C8H14N2O2S/c1-7-8(6-9)4-3-5-10(7)13(2,11)12/h7-8H,3-5H2,1-2H3/t7-,8+/m1/s1
• InChIKey: FANJRWOXJRSBJO-SFYZADRCSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC1C(CCCN1S(=O)(=O)C)C#N
  OpenEye OEToolkits 2.0.7: C[C@@H]1[C@@H](CCCN1S(=O)(=O)C)C#N
  CACTVS 3.385: C[CH]1[CH](CCCN1[S](C)(=O)=O)C#N
  CACTVS 3.385: C[C@@H]1[C@@H](CCCN1[S](C)(=O)=O)C#N
  ACDLabs 12.01: N#CC1CCCN(C1C)S(=O)(C)=O
• Formula: C8 H14 N2 O2 S
• Name: (2R,3R)-2-methyl-1-(methylsulfonyl)piperidine-3-carbonitrile
• PDB chain: 5s3q Chain B Residue 602

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5s3q Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.09 Å
• Binding residue (original residue number in PDB): L108 S111
• Binding residue (residue number reindexed from 1): L104 S107
• 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:5s3q, PDBe:5s3q, PDBj:5s3q
• PDBsum: 5s3q
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)