Structure of PDB 8tph Chain A Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: JKL
• InChI: InChI=1S/C27H37N3O3/c1-19(31)17-24(32)30(23-14-12-21(13-15-23)27(2,3)4)25(20-9-8-16-28-18-20)26(33)29-22-10-6-5-7-11-22/h8-9,12-16,18-19,22,25,31H,5-7,10-11,17H2,1-4H3,(H,29,33)/t19-,25-/m1/s1
• InChIKey: FQCVOMNESMUUJL-KBMIEXCESA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: C[C@H](CC(=O)N(c1ccc(cc1)C(C)(C)C)[C@H](c2cccnc2)C(=O)NC3CCCCC3)O
  ACDLabs 12.01: CC(C)(C)c1ccc(cc1)N(C(=O)CC(C)O)C(c1cccnc1)C(=O)NC1CCCCC1
  CACTVS 3.385: C[CH](O)CC(=O)N([CH](C(=O)NC1CCCCC1)c2cccnc2)c3ccc(cc3)C(C)(C)C
  CACTVS 3.385: C[C@@H](O)CC(=O)N([C@@H](C(=O)NC1CCCCC1)c2cccnc2)c3ccc(cc3)C(C)(C)C
  OpenEye OEToolkits 2.0.7: CC(CC(=O)N(c1ccc(cc1)C(C)(C)C)C(c2cccnc2)C(=O)NC3CCCCC3)O
• Formula: C27 H37 N3 O3
• Name: (3R)-N-(4-tert-butylphenyl)-N-[(1R)-2-(cyclohexylamino)-2-oxo-1-(pyridin-3-yl)ethyl]-3-hydroxybutanamide
• PDB chain: 8tph Chain A Residue 500

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8tph Design, Synthesis, X-ray Crystallography, and Biological Activities of Covalent, Non-Peptidic Inhibitors of SARS-CoV-2 Main Protease.
• Resolution: 1.52 Å
• Binding residue (original residue number in PDB): H41 F140 L141 N142 G143 C145 H163 M165 E166 D187 Q189
• Binding residue (residue number reindexed from 1): H41 F140 L141 N142 G143 C145 H163 M165 E166 D187 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:8tph, PDBe:8tph, PDBj:8tph
• PDBsum: 8tph
• PubMed: 38192109
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)