Structure of PDB 8upv Chain A Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: X83
• InChI: InChI=1S/C24H41FN4O6/c1-13(25)10-11-16(18(30)21(32)26-5)27-20(31)17-15-9-7-8-14(15)12-29(17)22(33)19(24(2,3)4)28-23(34)35-6/h13-19,30H,7-12H2,1-6H3,(H,26,32)(H,27,31)(H,28,34)/t13-,14+,15+,16+,17+,18-,19-/m1/s1
• InChIKey: RMJXELKXXMTVDO-JXBLTTDBSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: C[C@H](CC[C@@H]([C@H](C(=O)NC)O)NC(=O)[C@@H]1[C@H]2CCC[C@H]2CN1C(=O)[C@H](C(C)(C)C)NC(=O)OC)F
  CACTVS 3.385: CNC(=O)[CH](O)[CH](CC[CH](C)F)NC(=O)[CH]1[CH]2CCC[CH]2CN1C(=O)[CH](NC(=O)OC)C(C)(C)C
  OpenEye OEToolkits 2.0.7: CC(CCC(C(C(=O)NC)O)NC(=O)C1C2CCCC2CN1C(=O)C(C(C)(C)C)NC(=O)OC)F
  ACDLabs 12.01: CNC(=O)C(O)C(CCC(C)F)NC(=O)C1C2CCCC2CN1C(=O)C(NC(=O)OC)C(C)(C)C
  CACTVS 3.385: CNC(=O)[C@H](O)[C@H](CC[C@@H](C)F)NC(=O)[C@@H]1[C@H]2CCC[C@H]2CN1C(=O)[C@@H](NC(=O)OC)C(C)(C)C
• Formula: C24 H41 F N4 O6
• Name: methyl {(2S)-1-[(1S,3aR,6aS)-1-{[(2R,3S,6R)-6-fluoro-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: 8upv Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8upv Invention of MK-7845, a SARS-CoV-2 3CL Protease Inhibitor Employing a Novel Difluorinated Glutamine Mimic.
• Resolution: 1.57 Å
• Binding residue (original residue number in PDB): H41 L141 G143 C145 H164 M165 E166 L167 D187 R188 Q189
• Binding residue (residue number reindexed from 1): H41 L141 G143 C145 H164 M165 E166 L167 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:8upv, PDBe:8upv, PDBj:8upv
• PDBsum: 8upv
• PubMed: 38365209
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)