MolNFT v1 · #188763 · protein
Crystal structure of the first bromodomain of human brdt in complex with the inhibitor ccd-956
7UBO · Bromodomain testis-specific protein: “Crystal structure of the first bromodomain of human brdt in complex with the inhibitor ccd-956”. X-ray diffraction, 1 ligand (MJN), 9 pockets (best druggability 0.83). MolNFT v1 #188763 on…
- PDB
- 7UBO
- Type
- protein
- Length
- 434 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain testis-specific protein
- UniProt
- Q58F21
- Ligands
- MJN
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 63% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain testis-specific protein | protein | 109 | 66% helix, 0% strand | Q58F21 |
| B | Bromodomain testis-specific protein | protein | 108 | 62% helix, 0% strand | Q58F21 |
| C | Bromodomain testis-specific protein | protein | 108 | 64% helix, 0% strand | Q58F21 |
| D | Bromodomain testis-specific protein | protein | 109 | 61% helix, 0% strand | Q58F21 |
Ligands and binding sites
- MJN · N-[(2R)-1-(methylamino)-3-{1-[(4-methyl-2-oxo-1,2-dihydroquinolin-6-yl)acetyl]piperidin-4-yl}-1-oxopropan-2-yl]-5-phenylpyridine-2-carboxamide · ligand · 4 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1048 | 0.83 | 0.84 | 83 | empty |
| 2 | 104 | 0.54 | 0.83 | 19 | empty |
| 3 | 111 | 0.53 | 0.82 | 20 | MJN |
| 4 | 125 | 0.53 | 0.81 | 25 | empty |
| 5 | 227 | 0.52 | 0.76 | 33 | MJN |
Interfaces
5 interfaces between chains.
- C–D · 969 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 587 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 473 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 243 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 236 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7UBO · Crystal Structure of the first bromodomain of human BRDT in complex with the inhibitor… · the same entry in another collection · chain C against C, TM-score 1.00
- Q58F21 · AlphaFold monomer V2.0 prediction for bromodomain testis-specific protein (Q58F21) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 7UBO · PDBe 7UBO · UniProt Q58F21
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