Structure of PDB 8e6a Chain B Binding Site BS02

Receptor Information

>8e6a Chain B (length=296) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

FRKMAFPSGKVEGCMVQVTCGTTLNGLWLDDVVYCPRHVICTSEDMLNPN
YEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYKF
VRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNID
YDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVN
VLAWLYAAVINGDRWFLNFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLS
AQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

• Ligand ID: WJ0
• InChI: InChI=1S/C23H32ClN3O9S/c1-13(2)9-17(27-22(31)36-12-23(3,32)15-5-4-6-16(24)11-15)20(29)26-18(21(30)37(33,34)35)10-14-7-8-25-19(14)28/h4-6,8,11,13-14,17-18,21,30,32H,7,9-10,12H2,1-3H3,(H,26,29)(H,27,31)(H,33,34,35)/t14-,17-,18-,21+,23+/m0/s1
• InChIKey: ZBIMUYMJHGTCAY-BNVIUNNUSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CC=NC1=O)C(O)S(=O)(=O)O)NC(=O)OCC(C)(c2cccc(c2)Cl)O
  CACTVS 3.385: CC(C)C[CH](NC(=O)OC[C](C)(O)c1cccc(Cl)c1)C(=O)N[CH](C[CH]2CC=NC2=O)[CH](O)[S](O)(=O)=O
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OC[C@@](C)(O)c1cccc(Cl)c1)C(=O)N[C@@H](C[C@@H]2CC=NC2=O)[C@H](O)[S](O)(=O)=O
  ACDLabs 12.01: O=C1N=CCC1CC(NC(=O)C(CC(C)C)NC(=O)OCC(C)(O)c1cccc(Cl)c1)C(O)S(=O)(=O)O
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CC=NC1=O)[C@H](O)S(=O)(=O)O)NC(=O)OC[C@](C)(c2cccc(c2)Cl)O
• Formula: C23 H32 Cl N3 O9 S
• Name: (1R,2S)-2-[(N-{[(2S)-2-(3-chlorophenyl)-2-hydroxypropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl]propane-1-sulfonic acid
• PDB chain: 8e6a Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8e6a Structure-guided design of direct-acting antivirals that exploit the gem-dimethyl effect and potently inhibit 3CL proteases of severe acute respiratory syndrome Coronavirus-2 (SARS-CoV-2) and middle east respiratory syndrome coronavirus (MERS-CoV)
• Resolution: 2.05 Å
• Binding residue (original residue number in PDB): H41 F140 C145 H164 M165 E166 H172 D187 Q189 T190
• Binding residue (residue number reindexed from 1): H38 F137 C142 H161 M162 E163 H169 D184 Q186 T187
• 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.-

Gene Ontology

Molecular Function

• GO:0008233 peptidase activity

Biological Process

• GO:0019082 viral protein processing

External links

• PDB: RCSB:8e6a, PDBe:8e6a, PDBj:8e6a
• PDBsum: 8e6a
• PubMed: 37080108
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)