Structure of PDB 7lzz Chain A Binding Site BS02

Receptor Information

>7lzz Chain A (length=299) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS

Ligand information

• Ligand ID: YMV
• InChI: InChI=1S/C26H39N3O8S/c1-16(2)14-21(24(31)28-22(25(32)38(34,35)36)15-19-12-13-27-23(19)30)29-26(33)37-20-10-8-18(9-11-20)17-6-4-3-5-7-17/h3-7,16,18-22,25,32H,8-15H2,1-2H3,(H,27,30)(H,28,31)(H,29,33)(H,34,35,36)/t18-,19-,20-,21-,22-,25-/m0/s1
• InChIKey: GQBZOCZYIKJBAR-GAJBLSCZSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC2CCC(CC2)c3ccccc3
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OC2CCC(CC2)c3ccccc3
  CACTVS 3.385: CC(C)C[CH](NC(=O)O[CH]1CC[CH](CC1)c2ccccc2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](O)[S](O)(=O)=O
  CACTVS 3.385: CC(C)C[C@H](NC(=O)O[C@@H]1CC[C@H](CC1)c2ccccc2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](O)[S](O)(=O)=O
  ACDLabs 12.01: CC(C)CC(NC(=O)OC1CCC(CC1)c1ccccc1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
• Formula: C26 H39 N3 O8 S
• Name: (1S,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1r,4S)-4-phenylcyclohexyl)oxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid
• PDB chain: 7lzz Chain A Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7lzz Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.
• Resolution: 2.0 Å
• Binding residue (original residue number in PDB): H41 N142 C145 H163 H164 M165 E166 P168 D187 Q189
• Binding residue (residue number reindexed from 1): H39 N140 C143 H161 H162 M163 E164 P166 D185 Q187
• 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:7lzz, PDBe:7lzz, PDBj:7lzz
• PDBsum: 7lzz
• PubMed: 34865476
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)