Structure of PDB 5som Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: WVY
• InChI: InChI=1S/C17H19N3O3/c21-16(23-12-14-3-1-8-18-17(14)22)11-13-4-6-15(7-5-13)20-10-2-9-19-20/h2,4-7,9-10,14H,1,3,8,11-12H2,(H,18,22)/t14-/m0/s1
• InChIKey: BBSKBVDQKLCENN-AWEZNQCLSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1cnn(c1)c2ccc(cc2)CC(=O)OC[C@@H]3CCCNC3=O
  CACTVS 3.385: O=C(Cc1ccc(cc1)n2cccn2)OC[C@@H]3CCCNC3=O
  ACDLabs 12.01: c3nn(c2ccc(CC(OCC1C(NCCC1)=O)=O)cc2)cc3
  CACTVS 3.385: O=C(Cc1ccc(cc1)n2cccn2)OC[CH]3CCCNC3=O
  OpenEye OEToolkits 2.0.7: c1cnn(c1)c2ccc(cc2)CC(=O)OCC3CCCNC3=O
• Formula: C17 H19 N3 O3
• Name: [(3S)-2-oxopiperidin-3-yl]methyl [4-(1H-pyrazol-1-yl)phenyl]acetate
• PDB chain: 5som Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5som 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): D22 G48 V49 A52 G130
• Binding residue (residue number reindexed from 1): D20 G46 V47 A50 G128
• 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:5som, PDBe:5som, PDBj:5som
• PDBsum: 5som
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)