Structure of PDB 8ute Chain A Binding Site BS01

Receptor Information

>8ute Chain A (length=302) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SG

Ligand information

• Ligand ID: XKQ
• InChI: InChI=1S/C24H40F2N4O6/c1-23(2,3)18(29-22(35)36-6)21(34)30-12-13-8-7-9-14(13)16(30)19(32)28-15(10-11-24(4,25)26)17(31)20(33)27-5/h13-18,31H,7-12H2,1-6H3,(H,27,33)(H,28,32)(H,29,35)/t13-,14-,15-,16-,17+,18+/m0/s1
• InChIKey: WQJQYHZGBBCHOT-UXJCHEOYSA-N
• SMILES:
  ACDLabs 12.01: CNC(=O)C(O)C(CCC(C)(F)F)NC(=O)C1C2CCCC2CN1C(=O)C(NC(=O)OC)C(C)(C)C
  CACTVS 3.385: CNC(=O)[CH](O)[CH](CCC(C)(F)F)NC(=O)[CH]1[CH]2CCC[CH]2CN1C(=O)[CH](NC(=O)OC)C(C)(C)C
  OpenEye OEToolkits 2.0.7: CC(C)(C)[C@@H](C(=O)N1C[C@@H]2CCC[C@@H]2[C@H]1C(=O)N[C@@H](CCC(C)(F)F)[C@H](C(=O)NC)O)NC(=O)OC
  OpenEye OEToolkits 2.0.7: CC(C)(C)C(C(=O)N1CC2CCCC2C1C(=O)NC(CCC(C)(F)F)C(C(=O)NC)O)NC(=O)OC
  CACTVS 3.385: CNC(=O)[C@H](O)[C@H](CCC(C)(F)F)NC(=O)[C@@H]1[C@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)OC)C(C)(C)C
• Formula: C24 H40 F2 N4 O6
• Name: methyl {(2S)-1-[(1S,3aR,6aS)-1-{[(2R,3S)-6,6-difluoro-2-hydroxy-1-(methylamino)-1-oxoheptan-3-yl]carbamoyl}hexahydrocyclopenta[c]pyrrol-2(1H)-yl]-3,3-dimethyl-1-oxobutan-2-yl}carbamate
• PDB chain: 8ute Chain A Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ute Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic.
• Resolution: 1.45 Å
• Binding residue (original residue number in PDB): H41 M49 F140 L141 N142 G143 S144 C145 H164 M165 E166 D187 R188 Q189
• Binding residue (residue number reindexed from 1): H41 M49 F140 L141 N142 G143 S144 C145 H164 M165 E166 D187 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:8ute, PDBe:8ute, PDBj:8ute
• PDBsum: 8ute
• PubMed: 38365209
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)