Structure of PDB 7tj0 Chain A Binding Site BS01

Receptor Information

>7tj0 Chain A (length=301) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
S

Ligand information

• Ligand ID: S4L
• InChI: InChI=1S/C24H35N3O8S/c28-21-18(11-12-25-21)14-20(23(30)36(32,33)34)26-22(29)19(13-16-7-3-1-4-8-16)27-24(31)35-15-17-9-5-2-6-10-17/h2,5-6,9-10,16,18-20,23,30H,1,3-4,7-8,11-15H2,(H,25,28)(H,26,29)(H,27,31)(H,32,33,34)/t18-,19-,20-,23-/m0/s1
• InChIKey: JRFNCWJMGHZHFL-MXBUBSDBSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)COC(=O)N[C@@H](CC2CCCCC2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@H](O)S(=O)(=O)O
  CACTVS 3.385: O[CH]([CH](C[CH]1CCNC1=O)NC(=O)[CH](CC2CCCCC2)NC(=O)OCc3ccccc3)[S](O)(=O)=O
  CACTVS 3.385: O[C@H]([C@H](C[C@@H]1CCNC1=O)NC(=O)[C@H](CC2CCCCC2)NC(=O)OCc3ccccc3)[S](O)(=O)=O
  ACDLabs 12.01: O=C(OCc1ccccc1)NC(CC1CCCCC1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
  OpenEye OEToolkits 2.0.7: c1ccc(cc1)COC(=O)NC(CC2CCCCC2)C(=O)NC(CC3CCNC3=O)C(O)S(=O)(=O)O
• Formula: C24 H35 N3 O8 S
• Name: (1S,2S)-2-({N-[(benzyloxy)carbonyl]-3-cyclohexyl-L-alanyl}amino)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
• ZINC: ZINC000095598423
• PDB chain: 7tj0 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7tj0 Development of optimized drug-like small molecule inhibitors of the SARS-CoV-2 3CL protease for treatment of COVID-19.
• Resolution: 2.17 Å
• Binding residue (original residue number in PDB): M49 F140 G143 C145 H163 M165 E166 D187 R188
• Binding residue (residue number reindexed from 1): M49 F140 G143 C145 H163 M165 E166 D187 R188
• 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:7tj0, PDBe:7tj0, PDBj:7tj0
• PDBsum: 7tj0
• PubMed: 35393402
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)