Structure of PDB 7t43 Chain A Binding Site BS02

Receptor Information

>7t43 Chain A (length=299) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

GFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLN
PNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKY
KFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFN
IDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTIT
VNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILG
PLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

• Ligand ID: FP8
• InChI: InChI=1S/C28H40N4O9S/c1-17(2)10-21(25(35)30-22(26(36)42(38,39)40)12-19-8-9-29-24(19)34)31-27(37)41-20-13-28(14-20)15-32(16-28)23(33)11-18-6-4-3-5-7-18/h3-7,17,19-22,26,36H,8-16H2,1-2H3,(H,29,34)(H,30,35)(H,31,37)(H,38,39,40)/t19-,21-,22-,26+/m0/s1
• InChIKey: BUKWXURASAKBCJ-QOAPGFADSA-N
• SMILES:
  CACTVS 3.385: CC(C)C[CH](NC(=O)OC1CC2(C1)CN(C2)C(=O)Cc3ccccc3)C(=O)N[CH](C[CH]4CCNC4=O)[CH](O)[S](O)(=O)=O
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OC1CC2(C1)CN(C2)C(=O)Cc3ccccc3)C(=O)N[C@@H](C[C@@H]4CCNC4=O)[C@H](O)[S](O)(=O)=O
  ACDLabs 12.01: O=C(Cc1ccccc1)N1CC2(CC(C2)OC(=O)NC(CC(C)C)C(=O)NC(CC2CCNC2=O)C(O)S(=O)(=O)O)C1
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC2CC3(C2)CN(C3)C(=O)Cc4ccccc4
  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)OC2CC3(C2)CN(C3)C(=O)Cc4ccccc4
• Formula: C28 H40 N4 O9 S
• Name: (1R,2S)-1-hydroxy-2-[(N-{[(2-methyl-2-azaspiro[3.3]heptan-6-yl)oxy]carbonyl}-L-leucyl)amino]-3-[(3S)-2-oxopyrrolidin-3-yl]propane-1-sulfonic acid
• PDB chain: 7t43 Chain A Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7t43 Structure-Guided Design of Potent Spirocyclic Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3C-like Protease.
• Resolution: 1.7 Å
• Binding residue (original residue number in PDB): H41 F140 N142 C145 H163 H164 M165 E166 D187 Q189
• Binding residue (residue number reindexed from 1): H40 F139 N141 C144 H162 H163 M164 E165 D186 Q188
• 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:7t43, PDBe:7t43, PDBj:7t43
• PDBsum: 7t43
• PubMed: 35638577
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)