Structure of PDB 7m02 Chain B Binding Site BS02

Receptor Information

>7m02 Chain B (length=298) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

• Ligand ID: YKY
• InChI: InChI=1S/C21H28FN3O8S/c1-12(2)9-16(25-21(29)33-11-14-5-3-4-6-15(14)22)19(27)24-17(20(28)34(30,31)32)10-13-7-8-23-18(13)26/h3-6,8,12-13,16-17,20,28H,7,9-11H2,1-2H3,(H,24,27)(H,25,29)(H,30,31,32)/t13-,16-,17-,20+/m0/s1
• InChIKey: VAWJCTITNJHIPN-VZYKRBATSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CC=NC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2ccccc2F
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CC=NC1=O)C(O)S(=O)(=O)O)NC(=O)OCc2ccccc2F
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCc1ccccc1F)C(=O)N[CH](C[CH]2CC=NC2=O)[CH](O)[S](O)(=O)=O
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCc1ccccc1F)C(=O)N[C@@H](C[C@@H]2CC=NC2=O)[C@H](O)[S](O)(=O)=O
  ACDLabs 12.01: O=C1N=CCC1CC(NC(=O)C(CC(C)C)NC(=O)OCc1ccccc1F)C(O)S(=O)(=O)O
• Formula: C21 H28 F N3 O8 S
• Name: (1R,2S)-2-((S)-2-((((2-fluorobenzyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((R)-2-oxo-3,4-dihydro-2H-pyrrol-3-yl)propane-1-sulfonic acid
• PDB chain: 7m02 Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7m02 Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): H41 N142 C145 H163 H164 M165 E166 D187 Q189
• Binding residue (residue number reindexed from 1): H39 N140 C143 H161 H162 M163 E164 D185 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:7m02, PDBe:7m02, PDBj:7m02
• PDBsum: 7m02
• PubMed: 34865476
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)