Structure of PDB 8tbe Chain A Binding Site BS01

Receptor Information

>8tbe Chain A (length=306) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: ZQB
• InChI: InChI=1S/C23H28ClN5O3/c24-17-5-1-3-14-11-19(28-20(14)17)23(32)29-18(9-13-6-7-13)22(31)27-16(12-25)10-15-4-2-8-26-21(15)30/h1,3,5,11-13,15-16,18,25,28H,2,4,6-10H2,(H,26,30)(H,27,31)(H,29,32)/b25-12-/t15-,16-,18-/m0/s1
• InChIKey: IOEBZYOQTDUOBG-UZWGZPNFSA-N
• SMILES:
  CACTVS 3.385: Clc1cccc2cc([nH]c12)C(=O)N[C@@H](CC3CC3)C(=O)N[C@@H](C[C@@H]4CCCNC4=O)C=N
  ACDLabs 12.01: Clc1cccc2cc([NH]c21)C(=O)NC(CC1CC1)C(=O)NC(CC1CCCNC1=O)C=N
  OpenEye OEToolkits 2.0.7: c1cc2cc([nH]c2c(c1)Cl)C(=O)NC(CC3CC3)C(=O)NC(CC4CCCNC4=O)C=N
  OpenEye OEToolkits 2.0.7: [H]/N=C\[C@H](C[C@@H]1CCCNC1=O)NC(=O)[C@H](CC2CC2)NC(=O)c3cc4cccc(c4[nH]3)Cl
  CACTVS 3.385: Clc1cccc2cc([nH]c12)C(=O)N[CH](CC3CC3)C(=O)N[CH](C[CH]4CCCNC4=O)C=N
• Formula: C23 H28 Cl N5 O3
• Name: Pomotrelvir bound form
• PDB chain: 8tbe Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8tbe Evaluation of In Vitro Antiviral Activity of SARS-CoV-2 Mpro Inhibitor Pomotrelvir (PBI-0451) and Cross-Resistance to Nirmatrelvir Resistance Substitutions
• Resolution: 2.15 Å
• Binding residue (original residue number in PDB): H41 F140 C145 H163 H164 M165 E166 L167 P168 D187 R188 T190 A191
• Binding residue (residue number reindexed from 1): H41 F140 C145 H163 H164 M165 E166 L167 P168 D187 R188 T190 A191
• 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:8tbe, PDBe:8tbe, PDBj:8tbe
• PDBsum: 8tbe
• PubMed: 37800975
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)