Structure of PDB 8e61 Chain B Binding Site BS01

Receptor Information

>8e61 Chain B (length=300) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

GFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLN
PNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKY
KFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFN
IDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTIT
VNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILG
PLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS

Ligand information

• Ligand ID: VLU
• InChI: InChI=1S/C24H36ClN3O8S2/c1-14(2)10-18(28-23(32)36-13-24(3,4)37-17-7-5-6-16(25)12-17)21(30)27-19(22(31)38(33,34)35)11-15-8-9-26-20(15)29/h5-7,12,14-15,18-19,22,31H,8-11,13H2,1-4H3,(H,26,29)(H,27,30)(H,28,32)(H,33,34,35)/t15-,18-,19-,22+/m0/s1
• InChIKey: MOYGJNHMYWCTOO-SXTKRDDTSA-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)Sc2cccc(c2)Cl
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCC(C)(C)Sc1cccc(Cl)c1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)[S](O)(=O)=O
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCC(C)(C)Sc1cccc(Cl)c1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](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)Sc2cccc(c2)Cl
  ACDLabs 12.01: CC(C)CC(NC(=O)OCC(C)(C)Sc1cccc(Cl)c1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
• Formula: C24 H36 Cl N3 O8 S2
• Name: (1R,2S)-2-{[N-({2-[(3-chlorophenyl)sulfanyl]-2-methylpropoxy}carbonyl)-L-leucyl]amino}-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
• PDB chain: 8e61 Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8e61 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: 1.85 Å
• Binding residue (original residue number in PDB): H41 F140 N142 C145 H163 H164 M165 E166 D187 Q189
• Binding residue (residue number reindexed from 1): H40 F139 N141 C144 H162 H163 M164 E165 D186 Q188
• 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:8e61, PDBe:8e61, PDBj:8e61
• PDBsum: 8e61
• PubMed: 37080108
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)