Structure of PDB 7tix Chain A Binding Site BS01

Receptor Information

>7tix Chain A (length=302) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SG

Ligand information

• Ligand ID: Q56
• InChI: InChI=1S/C25H33N3O8S/c1-15(2)11-20(28-25(32)36-14-16-7-8-17-5-3-4-6-18(17)12-16)23(30)27-21(24(31)37(33,34)35)13-19-9-10-26-22(19)29/h3-8,12,15,19-21,24,31H,9-11,13-14H2,1-2H3,(H,26,29)(H,27,30)(H,28,32)(H,33,34,35)/t19-,20-,21-,24-/m0/s1
• InChIKey: KLDKNBLMZUYYLD-CIEVZJJWSA-N
• SMILES:
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCc1ccc2ccccc2c1)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2ccc3ccccc3c2
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](O)S(=O)(=O)O)NC(=O)OCc2ccc3ccccc3c2
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCc1ccc2ccccc2c1)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](O)[S](O)(=O)=O
  ACDLabs 12.01: CC(C)CC(NC(=O)OCc1cc2ccccc2cc1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
• Formula: C25 H33 N3 O8 S
• Name: N~2~-{[(naphthalen-2-yl)methoxy]carbonyl}-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
• PDB chain: 7tix Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7tix Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): F140 N142 C145 H163 H164 M165 E166 Q189
• Binding residue (residue number reindexed from 1): F140 N142 C145 H163 H164 M165 E166 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:7tix, PDBe:7tix, PDBj:7tix
• PDBsum: 7tix
• PubMed: 35393402
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)