Structure of PDB 8f2d Chain A Binding Site BS01

Receptor Information

>8f2d Chain A (length=306) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: XA8
• InChI: InChI=1S/C28H42F3N5O6/c1-26(2,3)21(33-25(42)28(29,30)31)24(41)36-13-15-18(27(15,4)5)19(36)22(39)32-16(14-35-10-7-6-9-17(35)37)20(38)23(40)34-11-8-12-34/h15-16,18-21,38H,6-14H2,1-5H3,(H,32,39)(H,33,42)/t15-,16-,18-,19-,20+,21+/m0/s1
• InChIKey: CEVFDXICNWCNKE-NLNBCDFGSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC1(C2C1C(N(C2)C(=O)C(C(C)(C)C)NC(=O)C(F)(F)F)C(=O)NC(CN3CCCCC3=O)C(C(=O)N4CCC4)O)C
  CACTVS 3.385: CC(C)(C)[CH](NC(=O)C(F)(F)F)C(=O)N1C[CH]2[CH]([CH]1C(=O)N[CH](CN3CCCCC3=O)[CH](O)C(=O)N4CCC4)C2(C)C
  ACDLabs 12.01: CC1(C)C2C(C(=O)NC(CN3CCCCC3=O)C(O)C(=O)N3CCC3)N(CC21)C(=O)C(NC(=O)C(F)(F)F)C(C)(C)C
  CACTVS 3.385: CC(C)(C)[C@H](NC(=O)C(F)(F)F)C(=O)N1C[C@H]2[C@@H]([C@H]1C(=O)N[C@@H](CN3CCCCC3=O)[C@@H](O)C(=O)N4CCC4)C2(C)C
  OpenEye OEToolkits 2.0.7: CC1([C@@H]2[C@H]1[C@H](N(C2)C(=O)[C@H](C(C)(C)C)NC(=O)C(F)(F)F)C(=O)N[C@@H](CN3CCCCC3=O)[C@H](C(=O)N4CCC4)O)C
• Formula: C28 H42 F3 N5 O6
• Name: (1R,2S,5S)-N-[(2S,3R)-4-(azetidin-1-yl)-3-hydroxy-4-oxo-1-(2-oxopiperidin-1-yl)butan-2-yl]-6,6-dimethyl-3-[3-methyl-N-(trifluoroacetyl)-L-valyl]-3-azabicyclo[3.1.0]hexane-2-carboxamide
• PDB chain: 8f2d Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8f2d Rational design of a new class of protease inhibitors for the potential treatment of coronavirus diseases
• Resolution: 1.95 Å
• Binding residue (original residue number in PDB): T26 H41 N142 G143 C145 H163 H164 M165 E166 L167 R188 Q189 T190
• Binding residue (residue number reindexed from 1): T26 H41 N142 G143 C145 H163 H164 M165 E166 L167 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:8f2d, PDBe:8f2d, PDBj:8f2d
• PDBsum: 8f2d
• PubMed: 38478629
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)