Research workbench
Crystal structure of the bromodomain of human crebbp bound to the benzodiazepinone G02778174
Analyse Crystal structure of the bromodomain of human crebbp bound to the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5I86
- Type
- protein
- Length
- 229 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Creb-binding protein
- UniProt
- Q92793
- Ligands
- 69A, SCN
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Creb-binding protein | protein | 115 | 67% helix, 0% strand | Q92793 |
| B | Creb-binding protein | protein | 114 | 68% helix, 0% strand | Q92793 |
Ligands and binding sites
- 69A · (4R)-N-benzyl-4-methyl-2-oxo-2,3,4,5-tetrahydro-1H-1,5-benzodiazepine-6-carboxamide · ligand · 2 copies · chains A, B
- SCN · Thiocyanate ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 362 | 0.62 | 0.78 | 28 | empty |
| 2 | 102 | 0.51 | 0.82 | 19 | EDO, 69A |
| 3 | 84 | 0.51 | 0.83 | 15 | 69A |
| 4 | 61 | 0.27 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 418 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 5I86 · Crystal structure of the bromodomain of human CREBBP bound to the benzodiazepi G02778174 · the same entry in another collection · chain A against A, TM-score 1.00
- Q92793 · AlphaFold monomer V2.0 prediction for creb-binding protein (Q92793) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q92793
- Elsewhere: RCSB PDB 5I86 · PDBe 5I86 · UniProt Q92793
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