Structure of PDB 7tq4 Chain A Binding Site BS01

Receptor Information

>7tq4 Chain A (length=293) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

MAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNPNYE
DLLIRKSNHNFLVQAGVQLRVIGHSMQNCVLKLKVDTANPKTPKYKFVRI
QPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNIDYDC
VSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITVNVLA
WLYAAVINGDRWFLNFTTTLNDFNLVAMKYNYEPLTQDHVDILGPLSAQT
GIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

• Ligand ID: IRZ
• InChI: InChI=1S/C24H32ClN3O5/c1-14(2)8-21(23(31)27-19(12-29)10-16-6-7-26-22(16)30)28-24(32)33-13-17-11-20(17)15-4-3-5-18(25)9-15/h3-5,9,12,14,16-17,19-21H,6-8,10-11,13H2,1-2H3,(H,26,30)(H,27,31)(H,28,32)/t16-,17-,19-,20-,21-/m0/s1
• InChIKey: MMZNSFGNZLNDCE-XYYCENQHSA-N
• SMILES:
  ACDLabs 12.01: Clc1cccc(c1)C1CC1COC(=O)NC(CC(C)C)C(=O)NC(CC1CCNC1=O)C=O
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OC[C@@H]1C[C@H]1c2cccc(Cl)c2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)C=O
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C=O)NC(=O)OCC2CC2c3cccc(c3)Cl
  CACTVS 3.385: CC(C)C[CH](NC(=O)OC[CH]1C[CH]1c2cccc(Cl)c2)C(=O)N[CH](C[CH]3CCNC3=O)C=O
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C=O)NC(=O)OC[C@@H]2C[C@H]2c3cccc(c3)Cl
• Formula: C24 H32 Cl N3 O5
• Name: N~2~-({[(1R,2R)-2-(3-chlorophenyl)cyclopropyl]methoxy}carbonyl)-N-{(2S)-1-oxo-3-[(3S)-2-oxopyrrolidin-3-yl]propan-2-yl}-L-leucinamide
• PDB chain: 7tq4 Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7tq4 Broad-Spectrum Cyclopropane-Based Inhibitors of Coronavirus 3C-like Proteases: Biochemical, Structural, and Virological Studies.
• Resolution: 2.45 Å
• Binding residue (original residue number in PDB): H41 F140 N142 G143 C145 H163 H164 M165 E166 P168 T190 A191
• Binding residue (residue number reindexed from 1): H36 F134 N136 G137 C139 H157 H158 M159 E160 P162 T184 A185
• 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:7tq4, PDBe:7tq4, PDBj:7tq4
• PDBsum: 7tq4
• PubMed: 36654747
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)