Research workbench
Crystal structure of the bromodomain of human crebbp in complex with a quinazolin-one ligand
Analyse Crystal structure of the bromodomain of human crebbp in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NYV
- Type
- protein
- Length
- 459 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Creb-binding protein
- UniProt
- Q92793
- Ligands
- 15E
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Creb-binding protein | protein | 116 | 67% helix, 0% strand | Q92793 |
| B | Creb-binding protein | protein | 115 | 68% helix, 0% strand | Q92793 |
| C, D | Creb-binding protein | protein | 114 | 69% helix, 0% strand | Q92793 |
Ligands and binding sites
- 15E · 6-bromo-3-methyl-3,4-dihydroquinazolin-2(1H)-one · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 351 | 0.66 | 0.80 | 45 | 15E |
| 2 | 632 | 0.66 | 0.76 | 58 | 15E |
| 3 | 74 | 0.49 | 0.83 | 16 | 15E |
| 4 | 84 | 0.48 | 0.82 | 18 | 15E |
| 5 | 94 | 0.35 | 0.74 | 15 | empty |
Interfaces
4 interfaces between chains.
- A–D · 546 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 492 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 242 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 114 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4NYV · Crystal Structure of the Bromodomain of human CREBBP in complex with a quinazolin-one… · the same entry in another collection · chain D against D, TM-score 1.00
- Q92793 · AlphaFold monomer V2.0 prediction for creb-binding protein (Q92793) · a predicted model of the same protein · chain D 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 4NYV · PDBe 4NYV · UniProt Q92793
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