Research workbench
Structural adaptation and conservation in quadruplex-drug recognition
Analyse Structural adaptation and conservation in quadruplex-drug recognition in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3CDM
- Type
- DNA
- Length
- 45 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*DT*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*D…
- Ligands
- NII, K
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA (5'- D(*DT*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*D GP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DG)-3') | dna | 22 | — | — |
| B | DNA (5'- D(*DT*DAP*DGP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DGP*DTP*DTP*DAP*D GP*DGP*DGP*DTP*DTP*DAP*DGP*DGP*DG)-3') | dna | 23 | — | — |
Ligands and binding sites
- NII · 2,7-bis[3-(dimethylamino)propyl]-4,9-bis[(3-hydroxypropyl)amino]benzo[lmn][3,8]phenanthroline-1,3,6,8(2H,7H)-tetrone · ligand · 6 copies · chains A, B
- K · Potassium ion · metal · 4 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.58 | 0.73 | 26 | NII |
Interfaces
1 interface between chains.
- A–B · 308 Ų buried · 12 hydrogen bonds · nucleic-nucleic
Compared structures
- 3CDM · Structural adaptation and conservation in quadruplex-drug recognition · 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 3CDM · PDBe 3CDM
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