Structure of PDB 7lkx Chain B Binding Site BS02

Receptor Information

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

FRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLNP
NYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKYK
FVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFNI
DYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTITV
NVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILGP
LSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS

Ligand information

• Ligand ID: Y71
• InChI: InChI=1S/C22H35N3O8S/c1-12(2)7-17(25-22(29)33-11-16-9-13-3-4-14(16)8-13)20(27)24-18(21(28)34(30,31)32)10-15-5-6-23-19(15)26/h3-4,12-18,21,28H,5-11H2,1-2H3,(H,23,26)(H,24,27)(H,25,29)(H,30,31,32)/t13-,14+,15-,16+,17-,18-,21-/m0/s1
• InChIKey: WZJYVJHLXCYWFV-JBKSVKCVSA-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)OC[C@H]2C[C@@H]3C[C@H]2C=C3
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OC[C@H]1C[C@@H]2C[C@H]1C=C2)C(=O)N[C@@H](C[C@@H]3CCNC3=O)[C@@H](O)[S](O)(=O)=O
  CACTVS 3.385: CC(C)C[CH](NC(=O)OC[CH]1C[CH]2C[CH]1C=C2)C(=O)N[CH](C[CH]3CCNC3=O)[CH](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)OCC2CC3CC2C=C3
• Formula: C22 H35 N3 O8 S
• Name: (1S,2S)-2-((S)-2-(((((1S,2S,4S)-bicyclo[2.2.1]hept-5-en-2-yl)methoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid
• PDB chain: 7lkx Chain B Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7lkx Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease.
• Resolution: 1.6 Å
• Binding residue (original residue number in PDB): H41 F140 N142 C145 H163 H164 M165 E166 D187 Q189
• Binding residue (residue number reindexed from 1): H39 F138 N140 C143 H161 H162 M163 E164 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:7lkx, PDBe:7lkx, PDBj:7lkx
• PDBsum: 7lkx
• PubMed: 34213885
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)