Structure of PDB 5d7y Chain C Binding Site BS02

Receptor Information

>5d7y Chain C (length=142) Species: 10419 (Hepatitis B virus subtype adyw)

MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASP
HHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNMGLKFRQL
LWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILST

Ligand information

• Ligand ID: 58H
• InChI: InChI=1S/C28H26ClFN4O3/c1-4-28(36,5-2)18-11-14-34(15-12-18)17-23-24(27(35)37-3)25(20-10-9-19(30)16-21(20)29)33-26(32-23)22-8-6-7-13-31-22/h1-2,6-10,13,16,18,25,36H,11-12,14-15,17H2,3H3,(H,32,33)
• InChIKey: GKZRJYVILONFJM-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.385: COC(=O)C1=C(CN2CC[CH](CC2)C(O)(C#C)C#C)NC(=N[CH]1c3ccc(F)cc3Cl)c4ccccn4
  CACTVS 3.385: COC(=O)C1=C(CN2CC[C@@H](CC2)C(O)(C#C)C#C)NC(=N[C@H]1c3ccc(F)cc3Cl)c4ccccn4
  OpenEye OEToolkits 1.9.2: COC(=O)C1=C(NC(=NC1c2ccc(cc2Cl)F)c3ccccn3)CN4CCC(CC4)C(C#C)(C#C)O
  ACDLabs 12.01: C(C(C4CCN(CC1=C(C(OC)=O)C(N=C(N1)c2ccccn2)c3c(Cl)cc(F)cc3)CC4)(O)C#C)#C
• Formula: C28 H26 Cl F N4 O3
• Name: methyl (4R)-4-(2-chloro-4-fluorophenyl)-6-{[4-(3-hydroxypenta-1,4-diyn-3-yl)piperidin-1-yl]methyl}-2-(pyridin-2-yl)-1,4-dihydropyrimidine-5-carboxylate
• PDB chain: 5d7y Chain C Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5d7y Hepatitis B Virus Capsids Have Diverse Structural Responses to Small-Molecule Ligands Bound to the Heteroaryldihydropyrimidine Pocket.
• Resolution: 3.894 Å
• Binding residue (original residue number in PDB): F23 T33 Y118
• Binding residue (residue number reindexed from 1): F23 T33 Y118
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005198 structural molecule activity

External links

• PDB: RCSB:5d7y, PDBe:5d7y, PDBj:5d7y
• PDBsum: 5d7y
• PubMed: 26842475
• UniProt: P03147|CAPSD_HBVD1 Capsid protein (Gene Name=C)