Structure of PDB 7lkt Chain B Binding Site BS02

Receptor Information

>7lkt Chain B (length=300) Species: 2697049 (Severe acute respiratory syndrome coronavirus 2)

GFRKMAFPSGKVEGCMVQVTCGTTTLNGLWLDDVVYCPRHVICTSEDMLN
PNYEDLLIRKSNHNFLVQAGNVQLRVIGHSMQNCVLKLKVDTANPKTPKY
KFVRIQPGQTFSVLACYNGSPSGVYQCAMRPNFTIKGSFLNGSCGSVGFN
IDYDCVSFCYMHHMELPTGVHAGTDLEGNFYGPFVDRQTAQAAGTDTTIT
VNVLAWLYAAVINGDRWFLNRFTTTLNDFNLVAMKYNYEPLTQDHVDILG
PLSAQTGIAVLDMCASLKELLQNGMNGRTILGSALLEDEFTPFDVVRQCS

Ligand information

• Ligand ID: Y4V
• InChI: InChI=1S/C25H41N3O8S/c1-14(2)5-19(22(30)27-20(23(31)37(33,34)35)9-18-3-4-26-21(18)29)28-24(32)36-13-25-10-15-6-16(11-25)8-17(7-15)12-25/h14-20,23,31H,3-13H2,1-2H3,(H,26,29)(H,27,30)(H,28,32)(H,33,34,35)/t15-,16+,17-,18-,19-,20-,23+,25-/m0/s1
• InChIKey: AFONNBAHWVWJGI-CLEZYGTASA-N
• SMILES:
  OpenEye OEToolkits 2.0.7: CC(C)CC(C(=O)NC(CC1CCNC1=O)C(O)S(=O)(=O)O)NC(=O)OCC23CC4CC(C2)CC(C4)C3
  CACTVS 3.385: CC(C)C[C@H](NC(=O)OCC12CC3CC(CC(C3)C1)C2)C(=O)N[C@@H](C[C@@H]4CCNC4=O)[C@H](O)[S](O)(=O)=O
  OpenEye OEToolkits 2.0.7: CC(C)C[C@@H](C(=O)N[C@@H](C[C@@H]1CCNC1=O)[C@H](O)S(=O)(=O)O)NC(=O)OCC23CC4CC(C2)CC(C4)C3
  ACDLabs 12.01: C(NC(C(NC(CC1C(=O)NCC1)CO)=O)CC(C)C)(=O)OCC24CC3CC(CC(C2)C3)C4
  CACTVS 3.385: CC(C)C[CH](NC(=O)OCC12CC3CC(CC(C3)C1)C2)C(=O)N[CH](C[CH]4CCNC4=O)[CH](O)[S](O)(=O)=O
• Formula: C25 H41 N3 O8 S
• Name: (1R,2S)-2-((S)-2-(((adamantan-1-ylmethoxy)carbonyl)amino)-4-methylpentanamido)-1-hydroxy-3-((S)-2-oxopyrrolidin-3-yl)propane-1-sulfonic acid
• PDB chain: 7lkt Chain B Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7lkt Structure-Guided Design of Conformationally Constrained Cyclohexane Inhibitors of Severe Acute Respiratory Syndrome Coronavirus-2 3CL Protease.
• Resolution: 1.5 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): H40 F139 N141 C144 H162 H163 M164 E165 D186 Q188
• 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:7lkt, PDBe:7lkt, PDBj:7lkt
• PDBsum: 7lkt
• PubMed: 34213885
• UniProt: P0DTD1|R1AB_SARS2 Replicase polyprotein 1ab (Gene Name=rep)