Structure of PDB 8e5z Chain B Binding Site BS01

Receptor Information

>8e5z Chain B (length=299) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS

Ligand information

• Ligand ID: WJB
• InChI: InChI=1S/C24H37N3O10S2/c1-15(2)12-18(21(29)26-19(22(30)39(34,35)36)13-16-10-11-25-20(16)28)27-23(31)37-14-24(3,4)38(32,33)17-8-6-5-7-9-17/h5-9,15-16,18-19,22,30H,10-14H2,1-4H3,(H,25,28)(H,26,29)(H,27,31)(H,34,35,36)/t16-,18-,19-,22+/m0/s1
• InChIKey: ATVOVJHWVGHVRU-JLEJFLCFSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC(C)(C)S(=O)(=O)c2ccccc2
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCC(C)(C)[S](=O)(=O)c1ccccc1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCC(C)(C)[S](=O)(=O)c1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)[S](O)(=O)=O
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](O)S(=O)(=O)O)NC(=O)OCC(C)(C)S(=O)(=O)c2ccccc2
  ACDLabs 12.01: CC(C)CC(NC(=O)OCC(C)(C)S(=O)(=O)c1ccccc1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
• Formula: C24 H37 N3 O10 S2
• Name: (1R,2S)-2-[(N-{[2-(benzenesulfonyl)-2-methylpropoxy]carbonyl}-L-leucyl)amino]-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
• PDB chain: 8e5z Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8e5z 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: 1.8 Å
• Binding residue (original residue number in PDB): H41 F140 N142 C145 H163 H164 M165 E166 L167 P168 D187 Q189 T190 Q192
• Binding residue (residue number reindexed from 1): H39 F138 N140 C143 H161 H162 M163 E164 L165 P166 D185 Q187 T188 Q190
• 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:8e5z, PDBe:8e5z, PDBj:8e5z
• PDBsum: 8e5z
• PubMed: 37080108
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)