Structure of PDB 7k0h Chain B Binding Site BS01

Receptor Information

>7k0h Chain B (length=300) Species: 694009 (Severe acute respiratory syndrome-related coronavirus)

GFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDTVYCPRHVICTAEDMLN
PNYEDLLIRKSNHSFLVQAGNVQLRVIGHSMQNCLLRLKVDTSNPKTPKY
KFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNHTIKGSFLNGSCGSVGFN
IDYDCVSFCYMHHMELPTGVHAGTDLEGKFYGPFVDRQTQAAGTDTTITL
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCAALKELLQNGMNGRTILGSTILEDEFTPFDVVRQCSG

Ligand information

• Ligand ID: VR4
• InChI: InChI=1S/C29H38N4O6/c1-19(2)15-24(33-29(38)39-18-21-11-7-4-8-12-21)27(36)32-23(16-22-13-14-30-26(22)35)25(34)28(37)31-17-20-9-5-3-6-10-20/h3-12,19,22-25,34H,13-18H2,1-2H3,(H,30,35)(H,31,37)(H,32,36)(H,33,38)/t22-,23-,24-,25+/m0/s1
• InChIKey: MPMTWRHFCLPCDF-OJJQZRKESA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(C(=O)NCc2ccccc2)O)NC(=O)OCc3ccccc3
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCc1ccccc1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)C(=O)NCc3ccccc3
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](O)C(=O)NCc3ccccc3
  ACDLabs 12.01: C(c1ccccc1)OC(NC(C(=O)NC(C(O)C(NCc2ccccc2)=O)CC3CCNC3=O)CC(C)C)=O
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](C(=O)NCc2ccccc2)O)NC(=O)OCc3ccccc3
• Formula: C29 H38 N4 O6
• Name: N-{(2S,3R)-4-(benzylamino)-3-hydroxy-4-oxo-1-[(3S)-2-oxopyrrolidin-3-yl]butan-2-yl}-N~2~-[(benzyloxy)carbonyl]-L-leucinamide;
  
• ZINC: GC376 alpha-ketoamide analog (bound form)
• PDB chain: 7k0h Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7k0h Postinfection treatment with a protease inhibitor increases survival of mice with a fatal SARS-CoV-2 infection.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): H41 F140 N142 G143 C145 H163 H164 M165 E166 Q189
• Binding residue (residue number reindexed from 1): H40 F139 N141 G142 C144 H162 H163 M164 E165 Q188
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.7.50: mRNA guanylyltransferase.
  3.4.19.12: ubiquitinyl hydrolase 1.
  3.4.22.-
  3.4.22.69: SARS coronavirus main proteinase.

Gene Ontology

Molecular Function

• GO:0008233 peptidase activity

Biological Process

• GO:0019082 viral protein processing

External links

• PDB: RCSB:7k0h, PDBe:7k0h, PDBj:7k0h
• PDBsum: 7k0h
• PubMed: 34210738
• UniProt: P0C6U8|R1A_SARS Replicase polyprotein 1a (Gene Name=1a)