Research workbench
An unexpected mode of small molecule DNA binding provides the structural basis for DNA cleavage by the potent antiproliferative agent (-)-lomaiviticin a
Analyse An unexpected mode of small molecule DNA binding provides the structural basis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2N96
- Type
- DNA
- Length
- 16 nucleotides
- Chains
- 2
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*C)-3')
- Ligands
- 4JF
- Pockets
- 1 · best druggability 0.23
Structure
solution nmr · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| X, Y | DNA (5'-D(*GP*CP*TP*AP*TP*AP*GP*C)-3') | dna | 8 | — | — |
Ligands and binding sites
- 4JF · (1R,1'R,2S,2'S,3R,3'R,5aR,10aR,11a'S)-2'-[(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)oxy]-2,2'-diethyl-11,11 '-dihydrazinyl-6,6',9,9'-tetrahydroxy-4,4',5,5',10,10'-hexaoxo-1,1'-bis{[2,4,6-trideoxy-4-(dimethylamino)-beta-L-arabino -hexopyranosyl]oxy}[2,2',3,3',4,4',5,5',5a,8,10,10',10a,11a'-tetradecahydro-1H,1'H-[3,3'-bibenzo[b]fluorene]]-2-yl 2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranoside · ligand · chains X, Y
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 | 50 | 0.23 | 0.72 | 8 | empty |
Interfaces
1 interface between chains.
- X–Y · 340 Ų buried · 28 hydrogen bonds · nucleic-nucleic
Compared structures
- 2N96 · An unexpected mode of small molecule DNA binding provides the structural basis for DNA… · the same entry in another collection · chain X against X, 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 2N96 · PDBe 2N96
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