Structure of PDB 7rvp Chain B Binding Site BS01

Receptor Information

>7rvp Chain B (length=306) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLAGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: 7VQ
• InChI: InChI=1S/C27H36N4O7/c1-17(2)23(31-27(36)38-16-18-7-4-3-5-8-18)26(35)30-22(14-21-9-6-12-37-21)25(34)29-20(15-32)13-19-10-11-28-24(19)33/h3-9,12,17,19-20,22-23,32H,10-11,13-16H2,1-2H3,(H,28,33)(H,29,34)(H,30,35)(H,31,36)/t19-,20-,22-,23-/m0/s1
• InChIKey: HGSMCFBUHVKHTG-SQOUVECCSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)C(C(=O)NC(Cc1ccco1)C(=O)NC(CC2CCNC2=O)CO)NC(=O)OCc3ccccc3
  CACTVS 3.385: CC(C)[CH](NC(=O)OCc1ccccc1)C(=O)N[CH](Cc2occc2)C(=O)N[CH](CO)C[CH]3CCNC3=O
  CACTVS 3.385: CC(C)[C@H](NC(=O)OCc1ccccc1)C(=O)N[C@@H](Cc2occc2)C(=O)N[C@H](CO)C[C@@H]3CCNC3=O
  ACDLabs 12.01: O=C1NCCC1CC(CO)NC(=O)C(NC(=O)C(NC(=O)OCc1ccccc1)C(C)C)Cc1ccco1
  OpenEye OEToolkits 2.0.7: CC(C)[C@@H](C(=O)N[C@@H](Cc1ccco1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)CO)NC(=O)OCc3ccccc3
• Formula: C27 H36 N4 O7
• Name: N-[(benzyloxy)carbonyl]-L-valyl-3-furan-2-yl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-alaninamide
• PDB chain: 7rvp Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7rvp A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.
• Resolution: 1.9 Å
• Binding residue (original residue number in PDB): H41 M49 F140 G143 C145 H163 H164 M165 E166 D187 Q189 T190
• Binding residue (residue number reindexed from 1): H41 M49 F140 G143 C145 H163 H164 M165 E166 D187 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:7rvp, PDBe:7rvp, PDBj:7rvp
• PDBsum: 7rvp
• PubMed: 35779291
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)