Structure of PDB 5sp3 Chain A Binding Site BS01

Receptor Information

>5sp3 Chain A (length=167) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

VNSFSGYLKLTDNVYIKNADIVEEAKKVKPTVVVNAANVYLKHGGGVAGA
LNKATNNAMQVESDDYIATNGPLKVGGSCVLSGHNLAKHCLHVVGPNVNK
GEDIQLLKSAYENFNQHEVLLAPLLSAGIFGADPIHSLRVCVDTVRTNVY
LAVFDKNLYDKLVSSFL

Ligand information

• Ligand ID: WYJ
• InChI: InChI=1S/C16H18N4O2/c1-10-6-20(7-11(8-21)22-10)16-14-12-4-2-3-5-13(12)19-15(14)17-9-18-16/h2-5,9-11,21H,6-8H2,1H3,(H,17,18,19)/t10-,11+/m1/s1
• InChIKey: SSHCMXMCAMBDLI-MNOVXSKESA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC1CN(CC(O1)CO)c2c3c4ccccc4[nH]c3ncn2
  OpenEye OEToolkits 2.0.7: C[C@@H]1CN(C[C@H](O1)CO)c2c3c4ccccc4[nH]c3ncn2
  CACTVS 3.385: C[CH]1CN(C[CH](CO)O1)c2ncnc3[nH]c4ccccc4c23
  ACDLabs 12.01: c4cc2c(c1c(ncnc1n2)N3CC(C)OC(CO)C3)cc4
  CACTVS 3.385: C[C@@H]1CN(C[C@@H](CO)O1)c2ncnc3[nH]c4ccccc4c23
• Formula: C16 H18 N4 O2
• Name: [(2S,6R)-6-methyl-4-(9H-pyrimido[4,5-b]indol-4-yl)morpholin-2-yl]methanol
• PDB chain: 5sp3 Chain A Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5sp3 Iterative computational design and crystallographic screening identifies potent inhibitors targeting the Nsp3 macrodomain of SARS-CoV-2.
• Resolution: 1.01 Å
• Binding residue (original residue number in PDB): I23 G48 V49 A52 A129 G130 I131 F156
• Binding residue (residue number reindexed from 1): I21 G46 V47 A50 A127 G128 I129 F154
• 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:5sp3, PDBe:5sp3, PDBj:5sp3
• PDBsum: 5sp3
• PubMed: 36598939
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)