Structure of PDB 6bvf Chain C Binding Site BS01

Receptor Information

>6bvf Chain C (length=142) Species: 10419 (Hepatitis B virus subtype adyw)

MDIDPYKEFGATVELLSFLPSDFFPSVRDLLDTAAALYRDALESPEHASP
HHTALRQAILAWGDLMTLATWVGTNLEDPASRDLVVSYVNTNVGLKFRQL
LWFHISALTFGRETVLEYLVSFGVWIRTPPAYRPPNAPILST

Ligand information

• Ligand ID: E9D
• InChI: InChI=1S/C51H48ClFN8O7/c1-58(2)32-13-17-36-42(27-32)68-43-28-33(59(3)4)14-18-37(43)45(36)38-25-30(11-15-34(38)50(64)65)49(63)55-20-8-10-44(62)61-23-21-60(22-24-61)29-41-46(51(66)67-5)47(35-16-12-31(53)26-39(35)52)57-48(56-41)40-9-6-7-19-54-40/h6-7,9,11-19,25-28H,8,10,20-24,29H2,1-5H3,(H-,55,63,64,65)
• InChIKey: PZTNESDVJNEZKJ-UHFFFAOYSA-N
• SMILES:
  ACDLabs 12.01: O=C(OC)c1c(nc(nc1CN1CCN(CC1)C(=O)CCCNC(=O)c1cc(C=2c3ccc(cc3OC3=CC(\C=CC=23)=[N+](/C)C)N(C)C)c(cc1)C([O-])=O)c1ccccn1)c1ccc(F)cc1Cl
  OpenEye OEToolkits 2.0.7: CN(C)c1ccc2c(c1)OC3=CC(=[N+](C)C)C=CC3=C2c4cc(ccc4C(=O)[O-])C(=O)NCCCC(=O)N5CCN(CC5)Cc6c(c(nc(n6)c7ccccn7)c8ccc(cc8Cl)F)C(=O)OC
  CACTVS 3.385: COC(=O)c1c(CN2CCN(CC2)C(=O)CCCNC(=O)c3ccc(C([O-])=O)c(c3)C4=C5C=CC(C=C5Oc6cc(ccc46)N(C)C)=[N+](C)C)nc(nc1c7ccc(F)cc7Cl)c8ccccn8
• Formula: C51 H48 Cl F N8 O7
• Name: Heteroaryldihydropyrimidine tetramethylrodamine;
  HAP-TAMRA
• PDB chain: 6bvf Chain B Residue 201

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6bvf Hepatitis B virus core protein allosteric modulators can distort and disrupt intact capsids.
• Resolution: 4.0 Å
• Binding residue (original residue number in PDB): V124 P129 P134
• Binding residue (residue number reindexed from 1): V124 P129 P134
• Annotation score: 1

Gene Ontology

Molecular Function

• GO:0005198 structural molecule activity

External links

• PDB: RCSB:6bvf, PDBe:6bvf, PDBj:6bvf
• PDBsum: 6bvf
• PubMed: 29377794
• UniProt: P03147|CAPSD_HBVD1 Capsid protein (Gene Name=C)