Structure of PDB 7faz Chain A Binding Site BS01

Receptor Information

>7faz Chain A (length=301) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
S

Ligand information

• Ligand ID: 2RI
• InChI: InChI=1S/C30H26FN3O4/c1-18(20-9-11-22(31)12-10-20)33-29(36)28(21-6-5-15-32-17-21)34(30(37)19(2)35)23-13-14-25-24-7-3-4-8-26(24)38-27(25)16-23/h3-19,28,35H,1-2H3,(H,33,36)/t18-,19+,28+/m0/s1
• InChIKey: ZZPWEZVCHNBBBZ-DORSKGMSSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(c1ccc(cc1)F)NC(=O)C(c2cccnc2)N(c3ccc4c5ccccc5oc4c3)C(=O)C(C)O
  OpenEye OEToolkits 2.0.7: C[C@@H](c1ccc(cc1)F)NC(=O)[C@@H](c2cccnc2)N(c3ccc4c5ccccc5oc4c3)C(=O)[C@@H](C)O
  CACTVS 3.385: C[C@@H](O)C(=O)N([C@@H](C(=O)N[C@@H](C)c1ccc(F)cc1)c2cccnc2)c3ccc4c(oc5ccccc45)c3
  CACTVS 3.385: C[CH](O)C(=O)N([CH](C(=O)N[CH](C)c1ccc(F)cc1)c2cccnc2)c3ccc4c(oc5ccccc45)c3
• Formula: C30 H26 F N3 O4
• Name: (2~{R})-~{N}-dibenzofuran-3-yl-~{N}-[(1~{R})-2-[[(1~{S})-1-(4-fluorophenyl)ethyl]amino]-2-oxidanylidene-1-pyridin-3-yl-ethyl]-2-oxidanyl-propanamide
• PDB chain: 7faz Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7faz An orally available M pro inhibitor is effective against wild-type SARS-CoV-2 and variants including Omicron.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): H41 M49 F140 L141 N142 G143 S144 C145 H163 H164 M165 E166 D187 R188 Q189
• Binding residue (residue number reindexed from 1): H41 M49 F140 L141 N142 G143 S144 C145 H163 H164 M165 E166 D187 R188 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:7faz, PDBe:7faz, PDBj:7faz
• PDBsum: 7faz
• PubMed: 35477751
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)