Structure of PDB 8rjy Chain A Binding Site BS01

Receptor Information

>8rjy Chain A (length=301) Species: 2901879 (Severe acute respiratory syndrome coronavirus)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
S

Ligand information

• Ligand ID: A1H1K
• InChI: InChI=1S/C29H34ClN5O3S/c1-29(2,3)25(33-26(36)24-11-8-16-39-24)27(37)32-23(17-20-9-6-5-7-10-20)28(38)34(4)35(19-31)18-21-12-14-22(30)15-13-21/h5-16,19,23,25,31H,17-18H2,1-4H3,(H,32,37)(H,33,36)/b31-19-/t23-,25+/m0/s1
• InChIKey: KRDFOVBETAPJMT-JNNRUENRSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)(C)C(C(=O)NC(Cc1ccccc1)C(=O)N(C)N(Cc2ccc(cc2)Cl)C=N)NC(=O)c3cccs3
  OpenEye OEToolkits 2.0.7: [H]/N=C\N(Cc1ccc(cc1)Cl)N(C)C(=O)[C@H](Cc2ccccc2)NC(=O)[C@H](C(C)(C)C)NC(=O)c3cccs3
  CACTVS 3.385: CN(N(Cc1ccc(Cl)cc1)C=N)C(=O)[C@H](Cc2ccccc2)NC(=O)[C@@H](NC(=O)c3sccc3)C(C)(C)C
  CACTVS 3.385: CN(N(Cc1ccc(Cl)cc1)C=N)C(=O)[CH](Cc2ccccc2)NC(=O)[CH](NC(=O)c3sccc3)C(C)(C)C
• Formula: C29 H34 Cl N5 O3 S
• Name: ~{N}-[(2~{S})-1-[[(2~{S})-1-[[(4-chlorophenyl)methyl-(iminomethyl)amino]-methyl-amino]-1-oxidanylidene-3-phenyl-propan-2-yl]amino]-3,3-dimethyl-1-oxidanylidene-butan-2-yl]thiophene-2-carboxamide
• PDB chain: 8rjy Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8rjy Macrocyclic Azapeptide Nitriles: Structure-Based Discovery of Potent SARS-CoV-2 Main Protease Inhibitors as Antiviral Drugs.
• Resolution: 1.97 Å
• Binding residue (original residue number in PDB): H41 M49 L141 N142 C145 H164 M165 E166 R188 Q189 T190
• Binding residue (residue number reindexed from 1): H41 M49 L141 N142 C145 H164 M165 E166 R188 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.-

External links

• PDB: RCSB:8rjy, PDBe:8rjy, PDBj:8rjy
• PDBsum: 8rjy
• PubMed: 38753594
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)