Structure of PDB 5s3u Chain A Binding Site BS01

Receptor Information

>5s3u Chain A (length=165) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGALN
KATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNKGE
DIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVYLA
VFDKNLYDKLVSSFL

Ligand information

• Ligand ID: W2J
• InChI: InChI=1S/C7H15NO/c1-6-2-7(5-9)4-8-3-6/h6-9H,2-5H2,1H3/t6-,7-/m1/s1
• InChIKey: SSKKCWRWVKPDIA-RNFRBKRXSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC1CC(CNC1)CO
  OpenEye OEToolkits 2.0.7: C[C@@H]1C[C@H](CNC1)CO
  CACTVS 3.385: C[CH]1CNC[CH](CO)C1
  CACTVS 3.385: C[C@H]1CNC[C@H](CO)C1
  ACDLabs 12.01: C1(CC(CO)CNC1)C
• Formula: C7 H15 N O
• Name: [(3R,5R)-5-methylpiperidin-3-yl]methanol
• ZINC: ZINC000107114818
• PDB chain: 5s3u Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5s3u Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.078 Å
• Binding residue (original residue number in PDB): S5 V30 K31
• Binding residue (residue number reindexed from 1): S1 V26 K27
• 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:5s3u, PDBe:5s3u, PDBj:5s3u
• PDBsum: 5s3u
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)