Research workbench
Crystal structure of the CBP bromodomain in complex with small molecule LC-CPin7
Analyse Crystal structure of the CBP bromodomain in complex with small molecule LC-CPin7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LQX
- Type
- protein
- Length
- 455 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.46
- Source
- Homo sapiens
- Molecule
- CREB-binding protein
- UniProt
- I3L466
- Ligands
- EOO, NA
- Pockets
- 9 · best druggability 0.60
Structure
x-ray diffraction · resolution 2.46 · 3 distinct chains · 67% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | CREB-binding protein | protein | 115 | 65% helix, 0% strand | I3L466 |
| D | CREB-binding protein | protein | 114 | 67% helix, 0% strand | I3L466 |
| C | CREB-binding protein | protein | 111 | 68% helix, 0% strand | I3L466 |
Ligands and binding sites
- EOO · (1~{S},6~{R})-6-[(1-methoxycarbonyl-3,4-dihydro-2~{H}-quinolin-6-yl)carbamoyl]cyclohex-3-ene-1-carboxylic acid · ligand · chains B
- NA · Sodium ion · metal · 6 copies · chains B, A, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 324 | 0.60 | 0.77 | 35 | empty |
| 2 | 69 | 0.51 | 0.85 | 21 | empty |
| 3 | 73 | 0.47 | 0.82 | 21 | empty |
| 4 | 83 | 0.46 | 0.81 | 18 | empty |
| 5 | 110 | 0.46 | 0.79 | 23 | EOO |
Interfaces
2 interfaces between chains.
- A–D · 1127 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 377 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6LQX · Crystal structure of the cbp bromodomain in complex with small molecule lc-CPIN7 · the same entry in another collection · chain A against A, TM-score 1.00
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 I3L466
- Elsewhere: RCSB PDB 6LQX · PDBe 6LQX · UniProt I3L466
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