Structure of PDB 8i30 Chain A Binding Site BS01

Receptor Information

>8i30 Chain A (length=304) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVT

Ligand information

• Ligand ID: OF9
• InChI: InChI=1S/C28H32F4N4O4/c29-27(30)11-9-19(10-12-27)26(40)36-17-28(31,32)15-22(36)24(38)35-21(14-18-6-2-1-3-7-18)23(37)25(39)34-16-20-8-4-5-13-33-20/h1-8,13,19,21-23,37H,9-12,14-17H2,(H,34,39)(H,35,38)/t21-,22-,23+/m1/s1
• InChIKey: QXLYQUMSFSBBGE-ZLNRFVROSA-N
• SMILES:
  CACTVS 3.385: O[C@@H]([C@@H](Cc1ccccc1)NC(=O)[C@H]2CC(F)(F)CN2C(=O)C3CCC(F)(F)CC3)C(=O)NCc4ccccn4
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)CC(C(C(=O)NCc2ccccn2)O)NC(=O)C3CC(CN3C(=O)C4CCC(CC4)(F)F)(F)F
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)C[C@H]([C@@H](C(=O)NCc2ccccn2)O)NC(=O)[C@H]3CC(CN3C(=O)C4CCC(CC4)(F)F)(F)F
  CACTVS 3.385: O[CH]([CH](Cc1ccccc1)NC(=O)[CH]2CC(F)(F)CN2C(=O)C3CCC(F)(F)CC3)C(=O)NCc4ccccn4
• Formula: C28 H32 F4 N4 O4
• Name: (2~{R})-1-[4,4-bis(fluoranyl)cyclohexyl]carbonyl-4,4-bis(fluoranyl)-~{N}-[(2~{R},3~{S})-3-oxidanyl-4-oxidanylidene-1-phenyl-4-(pyridin-2-ylmethylamino)butan-2-yl]pyrrolidine-2-carboxamide
• PDB chain: 8i30 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8i30 Discovery and structure-activity relationship studies of novel alpha-ketoamide derivatives targeting the SARS-CoV-2 main protease.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): T25 H41 M49 F140 L141 N142 G143 S144 C145 H163 H164 M165 E166 D187 R188
• Binding residue (residue number reindexed from 1): T25 H41 M49 F140 L141 N142 G143 S144 C145 H163 H164 M165 E166 D187 R188
• 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:8i30, PDBe:8i30, PDBj:8i30
• PDBsum: 8i30
• PubMed: 37517202
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)