MolNFT v1 · #107371 · DNA
Crystal structure of D(CGCGAATTCGCG)2 complexed with bph-1503
4U8A · DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3'): “Crystal structure of D(CGCGAATTCGCG)2 complexed with bph-1503”. X-ray diffraction, 2 ligands (3EZ, MG), 1 pocket (best druggability 0.28). MolNFT v1 #107371 on GenesisL1: 3D…
- PDB
- 4U8A
- Type
- DNA
- Length
- 24 nucleotides
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3')
- Ligands
- 3EZ, MG
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 1 distinct chain.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*TP*CP*GP*CP*G)-3') | dna | 12 | — | — |
Ligands and binding sites
- 3EZ · N,N'-bis[3-(1,4,5,6-tetrahydropyrimidin-2-yl)phenyl]biphenyl-4,4'-dicarboxamide · ligand · chains A, B
- MG · Magnesium ion · metal · 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 | 65 | 0.28 | 0.74 | 16 | 3EZ |
Interfaces
1 interface between chains.
- A–B · 563 Ų buried · 51 hydrogen bonds · nucleic-nucleic
Compared structures
- 4U8A · Crystal structure of D(CGCGAATTCGCG)2 complexed with BPH-1503 · 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 4U8A · PDBe 4U8A
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