Structure of PDB 8ftc Chain A Binding Site BS01

Receptor Information

>8ftc Chain A (length=306) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: Y8O
• InChI: InChI=1S/C24H37F2N5O4/c1-23(2,3)17(30-21(34)18(25)26)22(35)31-11-14-15(24(14,4)5)16(31)20(33)29-13(10-27)9-12-7-6-8-28-19(12)32/h10,12-18,27H,6-9,11H2,1-5H3,(H,28,32)(H,29,33)(H,30,34)/b27-10-/t12-,13-,14-,15-,16-,17+/m0/s1
• InChIKey: MSAKMAGHNICQTP-NJLGGNEPSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)F)C(=O)NC(CC3CCCNC3=O)C=N)C
  OpenEye OEToolkits 2.0.7: [H]/N=C\[C@H](C[C@@H]1CCCNC1=O)NC(=O)[C@@H]2[C@@H]3[C@@H](C3(C)C)CN2C(=O)[C@H](C(C)(C)C)NC(=O)C(F)F
  CACTVS 3.385: CC(C)(C)[C@H](NC(=O)C(F)F)C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](C[C@@H]3CCCNC3=O)C=N)C2(C)C
  CACTVS 3.385: CC(C)(C)[CH](NC(=O)C(F)F)C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](C[CH]3CCCNC3=O)C=N)C2(C)C
  ACDLabs 12.01: CC1(C)C2C(C(=O)NC(C=N)CC3CCCNC3=O)N(CC21)C(=O)C(NC(=O)C(F)F)C(C)(C)C
• Formula: C24 H37 F2 N5 O4
• Name: (1R,2S,5S)-3-[N-(difluoroacetyl)-3-methyl-L-valyl]-N-{(1Z,2S)-1-imino-3-[(3S)-2-oxopiperidin-3-yl]propan-2-yl}-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide
• PDB chain: 8ftc Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8ftc The Effect of Deuteration and Homologation of the Lactam Ring of Nirmatrelvir on Its Biochemical Properties and Oxidative Metabolism
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): H41 M49 F140 N142 G143 C145 H163 H164 M165 E166 D187 R188 Q189 T190
• Binding residue (residue number reindexed from 1): H41 M49 F140 N142 G143 C145 H163 H164 M165 E166 D187 R188 Q189 T190
• 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:8ftc, PDBe:8ftc, PDBj:8ftc
• PDBsum: 8ftc
• PubMed: 38144257
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)