MolNFT v1 · #170775 · protein
Crystal structure of the crebbp bromodomain in complex with a tetrahydroquinoxaline ligand
6YIK: “Crystal structure of the crebbp bromodomain in complex with a tetrahydroquinoxaline ligand”. X-ray diffraction, 1 ligand (OSQ), 5 pockets (best druggability 0.66). MolNFT v1 #170775 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6YIK
- Type
- protein
- Length
- 341 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Crebbp
- EC
- 2.3.1.48, 2.3.1.-
- UniProt
- Q92793
- Ligands
- OSQ
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Crebbp (EC 2.3.1.48, 2.3.1.-) | protein | 114 | 64% helix, 0% strand | Q92793 |
| C | Crebbp (EC 2.3.1.48, 2.3.1.-) | protein | 113 | 65% helix, 0% strand | Q92793 |
Ligands and binding sites
- OSQ · (3~{R})-~{N}-[3-(3,4-dihydro-2~{H}-quinolin-1-yl)-2,2-bis(fluoranyl)propyl]-3-methyl-2-oxidanylidene-3,4-dihydro-1~{H}-quinoxaline-5-carboxamide · ligand · 5 copies · chains A, C, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 262 | 0.66 | 0.82 | 34 | OSQ |
| 2 | 199 | 0.56 | 0.79 | 29 | empty |
| 3 | 64 | 0.51 | 0.85 | 16 | OSQ |
| 4 | 62 | 0.46 | 0.83 | 15 | OSQ |
| 5 | 80 | 0.31 | 0.73 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 355 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 301 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6YIK · Crystal structure of the CREBBP bromodomain in complex with a tetrahydroquinoxaline ligand · 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 A 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 6YIK · PDBe 6YIK · UniProt Q92793
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