Structure of PDB 8tpe Chain B Binding Site BS01

Receptor Information

>8tpe Chain B (length=305) Species: 2901879 (Severe acute respiratory syndrome coronavirus)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: JK0
• InChI: InChI=1S/C27H31N3O3/c1-27(2,3)22-11-13-23(14-12-22)30(24(32)15-17-31)25(21-10-7-16-28-19-21)26(33)29-18-20-8-5-4-6-9-20/h4-14,16,19,25,31H,15,17-18H2,1-3H3,(H,29,33)/t25-/m1/s1
• InChIKey: IEQMNFUCIIDFPY-RUZDIDTESA-N
• SMILES:
  ACDLabs 12.01: CC(C)(C)c1ccc(cc1)N(C(=O)CCO)C(c1cccnc1)C(=O)NCc1ccccc1
  OpenEye OEToolkits 2.0.7: CC(C)(C)c1ccc(cc1)N([C@H](c2cccnc2)C(=O)NCc3ccccc3)C(=O)CCO
  OpenEye OEToolkits 2.0.7: CC(C)(C)c1ccc(cc1)N(C(c2cccnc2)C(=O)NCc3ccccc3)C(=O)CCO
  CACTVS 3.385: CC(C)(C)c1ccc(cc1)N([CH](C(=O)NCc2ccccc2)c3cccnc3)C(=O)CCO
  CACTVS 3.385: CC(C)(C)c1ccc(cc1)N([C@@H](C(=O)NCc2ccccc2)c3cccnc3)C(=O)CCO
• Formula: C27 H31 N3 O3
• Name: N-[(1R)-2-(benzylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-N-(4-tert-butylphenyl)-3-hydroxypropanamide
• PDB chain: 8tpe Chain B Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8tpe Design, Synthesis, X-ray Crystallography, and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease.
• Resolution: 1.61 Å
• Binding residue (original residue number in PDB): H41 M49 F140 N142 G143 C145 H164 M165 E166 L167 P168
• Binding residue (residue number reindexed from 1): H41 M49 F140 N142 G143 C145 H164 M165 E166 L167 P168
• 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:8tpe, PDBe:8tpe, PDBj:8tpe
• PDBsum: 8tpe
• PubMed: 38192109
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)