Structure of PDB 5sqf Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: QQ9
• InChI: InChI=1S/C14H15N3O3/c18-13(17-7-1-2-9(8-17)14(19)20)11-4-6-16-12-10(11)3-5-15-12/h3-6,9H,1-2,7-8H2,(H,15,16)(H,19,20)/t9-/m1/s1
• InChIKey: ZNXPXZYKUWUFEH-SECBINFHSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1c[nH]c2c1c(ccn2)C(=O)N3CCC[C@H](C3)C(=O)O
  CACTVS 3.385: OC(=O)[CH]1CCCN(C1)C(=O)c2ccnc3[nH]ccc23
  CACTVS 3.385: OC(=O)[C@@H]1CCCN(C1)C(=O)c2ccnc3[nH]ccc23
  ACDLabs 12.01: O=C(c1ccnc2[NH]ccc21)N1CCCC(C1)C(=O)O
  OpenEye OEToolkits 2.0.7: c1c[nH]c2c1c(ccn2)C(=O)N3CCCC(C3)C(=O)O
• Formula: C14 H15 N3 O3
• Name: (3R)-1-(1H-pyrrolo[2,3-b]pyridine-4-carbonyl)piperidine-3-carboxylic acid
• PDB chain: 5sqf Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5sqf 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 V49 G130 A154 F156 D157
• Binding residue (residue number reindexed from 1): I21 V47 G128 A152 F154 D155
• 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:5sqf, PDBe:5sqf, PDBj:5sqf
• PDBsum: 5sqf
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)