Structure of PDB 8okm Chain B Binding Site BS01

Receptor Information

>8okm Chain B (length=305) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTF

Ligand information

• Ligand ID: 84C
• InChI: InChI=1S/C25H42N4O6/c1-14(2)19(28-24(34)35-25(3,4)5)23(33)29-12-16-7-6-8-18(16)20(29)22(32)27-17(13-30)11-15-9-10-26-21(15)31/h14-20,30H,6-13H2,1-5H3,(H,26,31)(H,27,32)(H,28,34)/t15-,16-,17-,18-,19-,20-/m0/s1
• InChIKey: MFQBHMWPFDDNFU-RABCQHRBSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)[C@@H](C(=O)N1C[C@@H]2CCC[C@@H]2[C@H]1C(=O)N[C@@H](C[C@@H]3CCNC3=O)CO)NC(=O)OC(C)(C)C
  CACTVS 3.385: CC(C)[CH](NC(=O)OC(C)(C)C)C(=O)N1C[CH]2CCC[CH]2[CH]1C(=O)N[CH](CO)C[CH]3CCNC3=O
  OpenEye OEToolkits 2.0.7: CC(C)C(C(=O)N1CC2CCCC2C1C(=O)NC(CC3CCNC3=O)CO)NC(=O)OC(C)(C)C
  CACTVS 3.385: CC(C)[C@H](NC(=O)OC(C)(C)C)C(=O)N1C[C@@H]2CCC[C@@H]2[C@H]1C(=O)N[C@H](CO)C[C@@H]3CCNC3=O
• Formula: C25 H42 N4 O6
• Name: tert-butyl-N-[(2S)-1-[(3S,3aS,6aR)-3-[[(2S)-1-oxidanyl-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]-3,3a,4,5,6,6a-hexahydro-1H-cyclopenta[c]pyrrol-2-yl]-3-methyl-1-oxidanylidene-butan-2-yl]carbamate;
  tert-butyl N-[(2S)-1-[(3S,3aS,6aR)-3-[[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepyrrolidin-3-yl]propan-2-yl]carbamoyl]-3,3a,4,5,6,6a-hexahydro-1H-cyclopenta[c]pyrrol-2-yl]-3-methyl-1-oxidanylidene-butan-2-yl]carbamate
• PDB chain: 8okm Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8okm Broad-spectrum coronavirus 3C-like protease peptidomimetic inhibitors effectively block SARS-CoV-2 replication in cells: Design, synthesis, biological evaluation, and X-ray structure determination.
• Resolution: 1.66 Å
• Binding residue (original residue number in PDB): H41 F140 L141 N142 G143 C145 H163 H164 M165 E166 Q189 T190 Q192
• Binding residue (residue number reindexed from 1): H41 F140 L141 N142 G143 C145 H163 H164 M165 E166 Q189 T190 Q192
• 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:8okm, PDBe:8okm, PDBj:8okm
• PDBsum: 8okm
• PubMed: 37043904
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)