Structure of PDB 7m03 Chain B Binding Site BS02

Receptor Information

>7m03 Chain B (length=299) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS

Ligand information

• Ligand ID: YLD
• InChI: InChI=1S/C21H30FN3O8S/c1-12(2)8-16(25-21(29)33-11-13-4-3-5-15(22)9-13)19(27)24-17(20(28)34(30,31)32)10-14-6-7-23-18(14)26/h3-5,9,12,14,16-17,20,28H,6-8,10-11H2,1-2H3,(H,23,26)(H,24,27)(H,25,29)(H,30,31,32)/t14-,16-,17-,20+/m0/s1
• InChIKey: LNGFVEUFXDACOC-JWWIWJDOSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2cccc(c2)F
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCc1cccc(F)c1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCc1cccc(F)c1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)[S](O)(=O)=O
  ACDLabs 12.01: CC(C)CC(NC(=O)OCc1cccc(F)c1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2cccc(c2)F
• Formula: C21 H30 F N3 O8 S
• Name: (1R,2S)-2-((S)-2-((((3-fluorobenzyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid
• ZINC: ZINC000095594449
• PDB chain: 7m03 Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7m03 Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): N142 C145 H163 H164 M165 E166 Q189
• Binding residue (residue number reindexed from 1): N140 C143 H161 H162 M163 E164 Q187
• 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:7m03, PDBe:7m03, PDBj:7m03
• PDBsum: 7m03
• PubMed: 34865476
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)