Structure of PDB 7rvr Chain A Binding Site BS01

Receptor Information

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

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLAGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SGVTFQ

Ligand information

• Ligand ID: 7W5
• InChI: InChI=1S/C28H44N4O6/c1-27(2,3)15-21(24(35)30-20(16-33)14-19-12-13-29-23(19)34)31-25(36)22(28(4,5)6)32-26(37)38-17-18-10-8-7-9-11-18/h7-11,19-22,33H,12-17H2,1-6H3,(H,29,34)(H,30,35)(H,31,36)(H,32,37)/t19-,20-,21-,22+/m0/s1
• InChIKey: BMXUTPCWTPHBMF-MYGLTJDJSA-N
• SMILES:
  CACTVS 3.385: CC(C)(C)C[C@H](NC(=O)[C@@H](NC(=O)OCc1ccccc1)C(C)(C)C)C(=O)N[C@H](CO)C[C@@H]2CCNC2=O
  OpenEye OEToolkits 2.0.7: CC(C)(C)CC(C(=O)NC(CC1CCNC1=O)CO)NC(=O)C(C(C)(C)C)NC(=O)OCc2ccccc2
  OpenEye OEToolkits 2.0.7: CC(C)(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)CO)NC(=O)[C@H](C(C)(C)C)NC(=O)OCc2ccccc2
  CACTVS 3.385: CC(C)(C)C[CH](NC(=O)[CH](NC(=O)OCc1ccccc1)C(C)(C)C)C(=O)N[CH](CO)C[CH]2CCNC2=O
  ACDLabs 12.01: CC(C)(C)C(NC(=O)OCc1ccccc1)C(=O)NC(CC(C)(C)C)C(=O)NC(CC1CCNC1=O)CO
• Formula: C28 H44 N4 O6
• Name: N-[(benzyloxy)carbonyl]-3-methyl-L-valyl-N-{(2S)-1-hydroxy-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-4-methyl-L-leucinamide
• PDB chain: 7rvr Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7rvr A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals.
• Resolution: 2.46 Å
• Binding residue (original residue number in PDB): H41 L141 N142 G143 C145 H163 H164 M165 E166 Q189 T190 A191
• Binding residue (residue number reindexed from 1): H41 L141 N142 G143 C145 H163 H164 M165 E166 Q189 T190 A191
• 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:7rvr, PDBe:7rvr, PDBj:7rvr
• PDBsum: 7rvr
• PubMed: 35779291
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)