Structure of PDB 7lzy Chain A Binding Site BS01

Receptor Information

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

FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS

Ligand information

• Ligand ID: YMJ
• InChI: InChI=1S/C23H41N3O8S/c1-4-5-15-6-8-17(9-7-15)34-23(30)26-18(12-14(2)3)21(28)25-19(22(29)35(31,32)33)13-16-10-11-24-20(16)27/h14-19,22,29H,4-13H2,1-3H3,(H,24,27)(H,25,28)(H,26,30)(H,31,32,33)/t15-,16-,17-,18-,19-,22+/m0/s1
• InChIKey: VCQYBHSDNWQLAS-ZXLNZJBRSA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CCCC1CCC(CC1)OC(=O)NC(CC(C)C)C(=O)NC(CC2CCNC2=O)C(O)S(=O)(=O)O
  CACTVS 3.385: CCC[C@@H]1CC[C@H](CC1)OC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](O)[S](O)(=O)=O
  CACTVS 3.385: CCC[CH]1CC[CH](CC1)OC(=O)N[CH](CC(C)C)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O
  OpenEye OEToolkits 2.0.7: CCCC1CCC(CC1)OC(=O)N[C@@H](CC(C)C)C(=O)N[C@@H](C[C@@H]2CCNC2=O)C(O)S(=O)(=O)O
  ACDLabs 12.01: CC(C)CC(NC(=O)OC1CCC(CCC)CC1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
• Formula: C23 H41 N3 O8 S
• Name: (1R,2S)-1-hydroxy-2-((S)-4-methyl-2-(((((1s,4S)-4-propylcyclohexyl)oxy)carbonyl)amino)pentanamido)-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid
• PDB chain: 7lzy Chain A Residue 401

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7lzy Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.
• Resolution: 1.85 Å
• Binding residue (original residue number in PDB): H41 M49 C145 H163 H164 M165 E166 P168 D187 Q189
• Binding residue (residue number reindexed from 1): H39 M47 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:7lzy, PDBe:7lzy, PDBj:7lzy
• PDBsum: 7lzy
• PubMed: 34865476
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)