MolNFT v1 · #121872 · protein
Crystal structure of the bromodomain of human crebbp bound to the benzodiazepinone G02778174
5I86 · Creb-binding protein: “Crystal structure of the bromodomain of human crebbp bound to the benzodiazepinone G02778174”. X-ray diffraction, 2 ligands (69A, SCN), 4 pockets (best druggability 0.62). MolNFT v1 #121872 on GenesisL1: 3D…
- 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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