Research workbench
Inhibiting the binding of class iia histone deacetylases to myocyte enhancer factor-2 by small molecules
Analyse Inhibiting the binding of class iia histone deacetylases to myocyte enhancer… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MU6
- Type
- protein + DNA
- Length
- 352 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Myocyte-specific enhancer factor 2A; DNA (5'- D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP…
- UniProt
- Q02078
- Ligands
- BXL
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Myocyte-specific enhancer factor 2A | protein | 71 | 49% helix, 17% strand | Q02078 |
| E, G | DNA (5'- D(*AP*AP*AP*GP*CP*TP*AP*TP*TP*AP*TP*TP*AP*GP*CP*TP*T)-3') | dna | 17 | — | — |
| F, H | DNA (5'- D(*TP*AP*AP*GP*CP*TP*AP*AP*TP*AP*AP*TP*AP*GP*CP*TP*T)-3') | dna | 17 | — | — |
Ligands and binding sites
- BXL · (3E)-N~8~-(2-aminophenyl)-N~1~-phenyloct-3-enediamide · ligand · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 724 | 0.65 | 0.74 | 52 | empty |
| 2 | 63 | 0.49 | 0.86 | 18 | empty |
| 3 | 152 | 0.41 | 0.74 | 21 | empty |
| 4 | 77 | 0.32 | 0.74 | 12 | empty |
| 5 | 61 | 0.28 | 0.74 | 15 | empty |
Interfaces
16 interfaces between chains.
- A–B · 2015 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2009 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 739 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- E–F · 739 Ų buried · 74 hydrogen bonds · nucleic-nucleic
- A–E · 549 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 3MU6 · Inhibiting the Binding of Class IIa Histone Deacetylases to Myocyte Enhancer Factor-2 by… · the same entry in another collection · chain H against H, TM-score 1.00
- Q02078 · AlphaFold monomer V2.0 prediction for myocyte-specific enhancer factor 2A (Q02078) · a predicted model of the same protein · chain A against A, TM-score 0.95
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q02078
- Elsewhere: RCSB PDB 3MU6 · PDBe 3MU6 · UniProt Q02078
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.