Structure of PDB 5spr Chain A Binding Site BS01

Receptor Information

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

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: S6C
• InChI: InChI=1S/C12H15N5O2/c18-9(19)4-8-2-1-3-17(5-8)12-10-11(14-6-13-10)15-7-16-12/h6-8H,1-5H2,(H,18,19)(H,13,14,15,16)/t8-/m0/s1
• InChIKey: OHVACHOAZRWEJX-QMMMGPOBSA-N
• SMILES:
  CACTVS 3.385: OC(=O)C[CH]1CCCN(C1)c2ncnc3nc[nH]c23
  ACDLabs 12.01: O=C(O)CC1CCCN(C1)c1ncnc2nc[NH]c12
  OpenEye OEToolkits 2.0.7: c1[nH]c2c(n1)ncnc2N3CCCC(C3)CC(=O)O
  OpenEye OEToolkits 2.0.7: c1[nH]c2c(n1)ncnc2N3CCC[C@H](C3)CC(=O)O
  CACTVS 3.385: OC(=O)C[C@@H]1CCCN(C1)c2ncnc3nc[nH]c23
• Formula: C12 H15 N5 O2
• Name: [(3S)-1-(7H-purin-6-yl)piperidin-3-yl]acetic acid
• PDB chain: 5spr Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5spr 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): G48 V49 G130 V155 F156 D157
• Binding residue (residue number reindexed from 1): G46 V47 G128 V153 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:5spr, PDBe:5spr, PDBj:5spr
• PDBsum: 5spr
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)