Structure of PDB 8uho Chain B Binding Site BS01

Receptor Information

>8uho Chain B (length=305) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: WTE
• InChI: InChI=1S/C34H42FN3O7/c1-22(2)17-29(31(39)36-27(20-28-9-6-15-43-28)19-25-14-16-44-33(25)41)37-32(40)30(18-23-10-12-26(35)13-11-23)38-34(42)45-21-24-7-4-3-5-8-24/h3-5,7-8,10-13,19,22,27-30H,6,9,14-18,20-21H2,1-2H3,(H,36,39)(H,37,40)(H,38,42)/b25-19-/t27-,28+,29+,30+/m1/s1
• InChIKey: MSFOIQNYTTYSCY-JIXKKDCZSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCCO1)C=C2CCOC2=O)NC(=O)C(Cc3ccc(cc3)F)NC(=O)OCc4ccccc4
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCCO1)/C=C\2/CCOC2=O)NC(=O)[C@H](Cc3ccc(cc3)F)NC(=O)OCc4ccccc4
  CACTVS 3.385: CC(C)C[CH](NC(=O)[CH](Cc1ccc(F)cc1)NC(=O)OCc2ccccc2)C(=O)N[CH](C[CH]3CCCO3)C=C4CCOC4=O
  CACTVS 3.385: CC(C)C[C@H](NC(=O)[C@H](Cc1ccc(F)cc1)NC(=O)OCc2ccccc2)C(=O)N[C@@H](C[C@@H]3CCCO3)/C=C4/CCOC4=O
  ACDLabs 12.01: Fc1ccc(cc1)CC(NC(=O)OCc1ccccc1)C(=O)NC(CC(C)C)C(=O)NC(CC1CCCO1)\C=C1\CCOC1=O
• Formula: C34 H42 F N3 O7
• Name: N-[(benzyloxy)carbonyl]-4-fluoro-L-phenylalanyl-N-[(2S,3Z)-1-[(2S)-oxolan-2-yl]-3-(2-oxooxolan-3-ylidene)propan-2-yl]-L-leucinamide;
  GSK4365096A
• PDB chain: 8uho Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8uho Exploration of the P1 residue in 3CL protease inhibitors leading to the discovery of a 2-tetrahydrofuran P1 replacement.
• Resolution: 2.02 Å
• Binding residue (original residue number in PDB): L27 H41 M49 F140 L141 N142 G143 C145 H163 H164 M165 E166 Q189 T190
• Binding residue (residue number reindexed from 1): L27 H41 M49 F140 L141 N142 G143 C145 H163 H164 M165 E166 Q189 T190
• 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:8uho, PDBe:8uho, PDBj:8uho
• PDBsum: 8uho
• PubMed: 38309201
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)