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N-terminal bromodomain of human BRD2 with N-(4-hydroxyphenyl) acetamide
Analyse N-terminal bromodomain of human BRD2 with N-(4-hydroxyphenyl) acetamide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4A9J
- Type
- protein
- Length
- 331 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain containing 2
- UniProt
- P25440
- Ligands
- TYL, SO4
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain containing 2 | protein | 112 | 63% helix, 0% strand | P25440 |
| B | Bromodomain containing 2 | protein | 113 | 59% helix, 0% strand | P25440 |
| C | Bromodomain containing 2 | protein | 106 | 65% helix, 0% strand | P25440 |
Ligands and binding sites
- TYL · N-(4-hydroxyphenyl)acetamide (tylenol) · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B, C
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 | 327 | 0.71 | 0.84 | 35 | TYL |
| 2 | 93 | 0.50 | 0.82 | 18 | TYL |
| 3 | 111 | 0.49 | 0.80 | 21 | EDO, TYL |
| 4 | 102 | 0.37 | 0.75 | 19 | empty |
| 5 | 68 | 0.34 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1104 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 350 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 132 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4A9J · N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N-(4-hydroxyphenyl) acetamide · the same entry in another collection · chain A against A, TM-score 1.00
- P25440 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 2 (P25440) · a predicted model of the same protein · chain B 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 P25440
- Elsewhere: RCSB PDB 4A9J · PDBe 4A9J · UniProt P25440
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