Structure of PDB 8e63 Chain B Binding Site BS01

Receptor Information

>8e63 Chain B (length=301) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
S

Ligand information

• Ligand ID: UV2
• InChI: InChI=1S/C22H33N3O8S2/c1-14(2)12-17(25-22(29)33-10-11-34-16-6-4-3-5-7-16)20(27)24-18(21(28)35(30,31)32)13-15-8-9-23-19(15)26/h3-7,14-15,17-18,21,28H,8-13H2,1-2H3,(H,23,26)(H,24,27)(H,25,29)(H,30,31,32)/t15-,17-,18-,21+/m0/s1
• InChIKey: AUIXPEVQDXBTHO-QUJKESNLSA-N
• SMILES:
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCCSc1ccccc1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCCSc1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)[S](O)(=O)=O
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCCSc2ccccc2
  ACDLabs 12.01: CC(C)CC(NC(=O)OCCSc1ccccc1)C(=O)NC(CC1CCNC1=O)C(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)OCCSc2ccccc2
• Formula: C22 H33 N3 O8 S2
• Name: (1R,2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]-2-[(N-{[2-(phenylsulfanyl)ethoxy]carbonyl}-L-leucyl)amino]propane-1-sulfonic acid
• PDB chain: 8e63 Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8e63 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: 1.75 Å
• Binding residue (original residue number in PDB): H41 N142 C145 H163 H164 E166 R188 Q189
• Binding residue (residue number reindexed from 1): H41 N142 C145 H163 H164 E166 R188 Q189
• 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:8e63, PDBe:8e63, PDBj:8e63
• PDBsum: 8e63
• PubMed: 37080108
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)