Structure of PDB 5s3t Chain B Binding Site BS01

Receptor Information

>5s3t Chain B (length=169) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SMVNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVA
GALNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNV
NKGEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTN
VYLAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: W2G
• InChI: InChI=1S/C10H12O2S/c11-10(12)9-3-1-2-8(9)7-4-5-13-6-7/h4-6,8-9H,1-3H2,(H,11,12)/t8-,9-/m1/s1
• InChIKey: GTNCFHPRVUWUBC-RKDXNWHRSA-N
• SMILES:
  ACDLabs 12.01: C2C(c1ccsc1)C(C(O)=O)CC2
  OpenEye OEToolkits 2.0.7: c1cscc1C2CCCC2C(=O)O
  OpenEye OEToolkits 2.0.7: c1cscc1[C@H]2CCC[C@H]2C(=O)O
  CACTVS 3.385: OC(=O)[CH]1CCC[CH]1c2cscc2
  CACTVS 3.385: OC(=O)[C@@H]1CCC[C@@H]1c2cscc2
• Formula: C10 H12 O2 S
• Name: (1R,2S)-2-(thiophen-3-yl)cyclopentane-1-carboxylic acid
• PDB chain: 5s3t Chain B Residue 601

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5s3t Fragment binding to the Nsp3 macrodomain of SARS-CoV-2 identified through crystallographic screening and computational docking.
• Resolution: 1.085 Å
• Binding residue (original residue number in PDB): V41 Y42 K102
• Binding residue (residue number reindexed from 1): V41 Y42 K102
• 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:5s3t, PDBe:5s3t, PDBj:5s3t
• PDBsum: 5s3t
• PubMed: 33853786
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)