Structure of PDB 5soi Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: WVG
• InChI: InChI=1S/C14H18N4O2/c19-12(20)4-3-10-2-1-7-18(8-10)14-11-5-6-15-13(11)16-9-17-14/h5-6,9-10H,1-4,7-8H2,(H,19,20)(H,15,16,17)/t10-/m1/s1
• InChIKey: ADFCTPSWZLLXQI-SNVBAGLBSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1c[nH]c2c1c(ncn2)N3CCCC(C3)CCC(=O)O
  OpenEye OEToolkits 2.0.7: c1c[nH]c2c1c(ncn2)N3CCC[C@@H](C3)CCC(=O)O
  CACTVS 3.385: OC(=O)CC[CH]1CCCN(C1)c2ncnc3[nH]ccc23
  ACDLabs 12.01: c21c(ncc1)ncnc2N3CCCC(CCC(O)=O)C3
  CACTVS 3.385: OC(=O)CC[C@H]1CCCN(C1)c2ncnc3[nH]ccc23
• Formula: C14 H18 N4 O2
• Name: 3-[(3R)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-3-yl]propanoic acid
• PDB chain: 5soi Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5soi 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 A129 G130 V155 F156 L160
• Binding residue (residue number reindexed from 1): I21 G46 V47 A127 G128 V153 F154 L158
• 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:5soi, PDBe:5soi, PDBj:5soi
• PDBsum: 5soi
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)