Structure of PDB 7lzu Chain B Binding Site BS01

Receptor Information

>7lzu Chain B (length=298) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC

Ligand information

• Ligand ID: YKP
• InChI: InChI=1S/C22H37F2N3O8S/c1-12(2)10-16(27-21(31)35-13(3)14-4-7-22(23,24)8-5-14)19(29)26-17(20(30)36(32,33)34)11-15-6-9-25-18(15)28/h12-17,20,30H,4-11H2,1-3H3,(H,25,28)(H,26,29)(H,27,31)(H,32,33,34)/t13-,15-,16-,17-,20-/m0/s1
• InChIKey: YRNJEPAFOLVHMN-ZZKADIETSA-N
• SMILES:
  CACTVS 3.385: CC(C)C[CH](NC(=O)O[CH](C)C1CCC(F)(F)CC1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O
  CACTVS 3.385: CC(C)C[C@H](NC(=O)O[C@@H](C)C1CCC(F)(F)CC1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@@H](O)[S](O)(=O)=O
  ACDLabs 12.01: CC(C)CC(NC(=O)OC(C)C1CCC(F)(F)CC1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC(C)C2CCC(CC2)(F)F
  OpenEye OEToolkits 2.0.7: C[C@@H](C1CCC(CC1)(F)F)OC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]2CCNC2=O)C(O)S(=O)(=O)O
• Formula: C22 H37 F2 N3 O8 S
• Name: (1S,2S)-2-((S)-2-((((S)-1-(4,4-difluorocyclohexyl)ethoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid
• PDB chain: 7lzu Chain B Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7lzu Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): H41 N142 G143 C145 H163 H164 M165 E166 P168 D187 Q189 A191
• Binding residue (residue number reindexed from 1): H39 N140 G141 C143 H161 H162 M163 E164 P166 D185 Q187 A189
• 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:7lzu, PDBe:7lzu, PDBj:7lzu
• PDBsum: 7lzu
• PubMed: 34865476
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)