Research workbench
Crebbp bromodomain in complex with cpd 4 (1-(1-(cyclopropylmethyl)-3- (1H-indol-4-yl)-1,4,6,7-tetrahydro-5H-PYRAZOLO[4,3-C]PYRIDIN-5-yl) ethan-1-one)
Analyse Crebbp bromodomain in complex with cpd 4 (1-(1-(cyclopropylmethyl)-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ALC
- Type
- protein
- Length
- 228 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Creb-binding protein
- EC
- 2.3.1.48
- UniProt
- Q92793
- Ligands
- BKD
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 68% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Creb-binding protein (EC 2.3.1.48) | protein | 114 | 68% helix, 0% strand | Q92793 |
Ligands and binding sites
- BKD · 1-[1-(cyclopropylmethyl)-3-(1H-indol-4-yl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl]ethan-1-one · ligand · chains B
- DMS · Dimethyl sulfoxide · additive · chains A
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 84 | 0.47 | 0.81 | 18 | DMS |
| 2 | 92 | 0.45 | 0.80 | 21 | BKD |
| 3 | 71 | 0.31 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 497 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6ALC · CREBBP bromodomain in complex with Cpd 4 (1-(1-(cyclopropylmethyl)-3-(1H-indol-4-yl)-1,4,6… · 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 6ALC · PDBe 6ALC · UniProt Q92793
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