Research workbench
DNA minor-groove recognition of a tris-benzimidazole drug
Analyse DNA minor-groove recognition of a tris-benzimidazole drug in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 459D
- Type
- DNA
- Length
- 24 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.3
- Molecule
- DNA (5'-D(*CP*GP*(CBR)P*AP*TP*AP*TP*TP*TP*GP*CP*G)-3'); DNA…
- Ligands
- TBZ
- Pockets
- 1 · best druggability 0.25
Structure
x-ray diffraction · resolution 2.3 · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'-D(*CP*GP*(CBR)P*AP*TP*AP*TP*TP*TP*GP*CP*G)-3') | dna | 12 | — | — |
| B | DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*AP*TP*GP*CP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- TBZ · 2''-(4-methoxyphenyl)-5-(3-amino-1-pyrrolidinyl)-2,5',2',5''-tri-benzimidazole · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 53 | 0.25 | 0.73 | 13 | TBZ |
Interfaces
1 interface between chains.
- A–B · 558 Ų buried · 58 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 459D · DNA minor-groove recognition of a tris-benzimidazole drug · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 459D · PDBe 459D
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.