Structure of PDB 7woh Chain B Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGV

Ligand information

• Ligand ID: 5IW
• InChI: InChI=1S/C32H40N4O5/c1-22(2)18-27(31(40)34-26(21-37)20-25-14-9-17-33-30(25)39)36-32(41)28(19-24-12-7-4-8-13-24)35-29(38)16-15-23-10-5-3-6-11-23/h3-8,10-13,15-16,21-22,25-28H,9,14,17-20H2,1-2H3,(H,33,39)(H,34,40)(H,35,38)(H,36,41)/t25-,26-,27-,28-/m0/s1
• InChIKey: ZRDHUXRBDHYVKZ-LJWNLINESA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCCNC1=O)C=O)NC(=O)C(Cc2ccccc2)NC(=O)C=Cc3ccccc3
  CACTVS 3.385: CC(C)C[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)\C=C\c2ccccc2)C(=O)N[C@@H](C[C@@H]3CCCNC3=O)C=O
  CACTVS 3.385: CC(C)C[CH](NC(=O)[CH](Cc1ccccc1)NC(=O)C=Cc2ccccc2)C(=O)N[CH](C[CH]3CCCNC3=O)C=O
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCCNC1=O)C=O)NC(=O)[C@H](Cc2ccccc2)NC(=O)/C=C/c3ccccc3
• Formula: C32 H40 N4 O5
• Name: (2S)-4-methyl-N-[(2S)-1-oxidanylidene-3-[(3S)-2-oxidanylidenepiperidin-3-yl]propan-2-yl]-2-[[(2S)-3-phenyl-2-[[(E)-3-phenylprop-2-enoyl]amino]propanoyl]amino]pentanamide
• PDB chain: 7woh Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7woh 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): F140 N142 G143 C145 H163 H164 M165 E166 P168 Q189
• Binding residue (residue number reindexed from 1): F140 N142 G143 C145 H163 H164 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:7woh, PDBe:7woh, PDBj:7woh
• PDBsum: 7woh
• PubMed: 35216507
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)