Research workbench
Crystal structure of brdt bromodomain 2 in complex with cdd-1302
Analyse Crystal structure of brdt bromodomain 2 in complex with cdd-1302 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7L99
- Type
- protein
- Length
- 450 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain testis-specific protein
- UniProt
- Q58F21
- Ligands
- XWJ, JEF
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Bromodomain testis-specific protein | protein | 113 | 68% helix, 0% strand | Q58F21 |
| B | Bromodomain testis-specific protein | protein | 111 | 69% helix, 0% strand | Q58F21 |
Ligands and binding sites
- XWJ · N-[3-(acetylamino)-4-methylphenyl]-3-(4-amino-2-methylphenyl)-1-methyl-1H-indazole-5-carboxamide · ligand · 6 copies · chains A, B, C, D
- JEF · O-(O-(2-aminopropyl)-O'-(2-methoxyethyl)polypropylene glycol 500) · ligand · chains B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1039 | 0.76 | 0.78 | 104 | XWJ, JEF |
| 2 | 340 | 0.60 | 0.77 | 37 | empty |
| 3 | 121 | 0.56 | 0.83 | 20 | XWJ |
| 4 | 124 | 0.55 | 0.82 | 24 | XWJ |
Interfaces
4 interfaces between chains.
- A–B · 683 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 422 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 264 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 117 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7L99 · Crystal structure of BRDT bromodomain 2 in complex with CDD-1302 · the same entry in another collection · chain D against D, TM-score 1.00
- Q58F21 · AlphaFold monomer V2.0 prediction for bromodomain testis-specific protein (Q58F21) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q58F21
- Elsewhere: RCSB PDB 7L99 · PDBe 7L99 · UniProt Q58F21
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