Structure of PDB 7wof Chain A Binding Site BS01

Receptor Information

>7wof Chain A (length=303) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGV

Ligand information

• Ligand ID: 5IZ
• InChI: InChI=1S/C23H31N3O4/c1-3-16(2)21(26-20(28)12-11-17-8-5-4-6-9-17)23(30)25-19(15-27)14-18-10-7-13-24-22(18)29/h4-6,8-9,11-12,15-16,18-19,21H,3,7,10,13-14H2,1-2H3,(H,24,29)(H,25,30)(H,26,28)/b12-11+/t16-,18-,19-,21-/m0/s1
• InChIKey: LLWUOBUNLOPRDK-VXUGWXBBSA-N
• SMILES:
  CACTVS 3.385: CC[CH](C)[CH](NC(=O)C=Cc1ccccc1)C(=O)N[CH](C[CH]2CCCNC2=O)C=O
  CACTVS 3.385: CC[C@H](C)[C@H](NC(=O)/C=C/c1ccccc1)C(=O)N[C@@H](C[C@@H]2CCCNC2=O)C=O
  OpenEye OEToolkits 2.0.7: CC[C@H](C)[C@@H](C(=O)N[C@@H](C[C@@H]1CCCNC1=O)C=O)NC(=O)/C=C/c2ccccc2
  OpenEye OEToolkits 2.0.7: CCC(C)C(C(=O)NC(CC1CCCNC1=O)C=O)NC(=O)C=Cc2ccccc2
• Formula: C23 H31 N3 O4
• Name: (2S,3S)-3-methyl-N-[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepiperidin-3-yl]propan-2-yl]-2-[[(E)-3-phenylprop-2-enoyl]amino]pentanamide
• PDB chain: 7wof Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7wof Discovery of SARS-CoV-2 3CL Pro Peptidomimetic Inhibitors through the Catalytic Dyad Histidine-Specific Protein-Ligand Interactions.
• Resolution: 1.72 Å
• Binding residue (original residue number in PDB): H41 M49 F140 G143 C145 H163 M165 E166 P168 Q189
• Binding residue (residue number reindexed from 1): H41 M49 F140 G143 C145 H163 M165 E166 P168 Q189
• 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:7wof, PDBe:7wof, PDBj:7wof
• PDBsum: 7wof
• PubMed: 35216507
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)