Structure of PDB 7lzx Chain B Binding Site BS02

Receptor Information

>7lzx Chain B (length=302) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

SGFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDML
NPNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPK
YKFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGF
NIDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTI
TVNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDIL
GPLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQC
SG

Ligand information

• Ligand ID: YMD
• InChI: InChI=1S/C22H39N3O8S/c1-13(2)11-16(25-21(29)33-15-5-8-22(3,4)9-6-15)19(27)24-17(20(28)34(30,31)32)12-14-7-10-23-18(14)26/h13-17,20,28H,5-12H2,1-4H3,(H,23,26)(H,24,27)(H,25,29)(H,30,31,32)/t14-,16-,17-,20+/m0/s1
• InChIKey: LGCFVMZACNBZBJ-JWWIWJDOSA-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)(C)C
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OC1CCC(C)(C)CC1)C(=O)N[C@@H](C[C@@H]2CCNC2=O)[C@H](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)OC2CCC(CC2)(C)C
  ACDLabs 12.01: CC(C)CC(NC(=O)OC1CCC(C)(C)CC1)C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O
  CACTVS 3.385: CC(C)C[CH](NC(=O)OC1CCC(C)(C)CC1)C(=O)N[CH](C[CH]2CCNC2=O)[CH](O)[S](O)(=O)=O
• Formula: C22 H39 N3 O8 S
• Name: (1R,2S)-2-((S)-2-((((4,4-dimethylcyclohexyl)oxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid
• PDB chain: 7lzx Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7lzx Structure-Guided Design of Potent Inhibitors of SARS-CoV-2 3CL Protease: Structural, Biochemical, and Cell-Based Studies.
• Resolution: 1.65 Å
• Binding residue (original residue number in PDB): F140 N142 C145 H163 H164 M165 E166 Q189
• Binding residue (residue number reindexed from 1): F140 N142 C145 H163 H164 M165 E166 Q189
• 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:7lzx, PDBe:7lzx, PDBj:7lzx
• PDBsum: 7lzx
• PubMed: 34865476
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)