MolNFT v1 · #58011 · protein
Crystal structure of the human BRD2 BD1 bromodomain in complex with a BRD2-interactive compound, BIC1
3AQA · Bromodomain-containing protein 2: “Crystal structure of the human BRD2 BD1 bromodomain in complex with a BRD2-interactive compound, BIC1”. X-ray diffraction, 1 ligand (BYH), 7 pockets (best druggability 0.70). MolNFT v1 #58011 on…
- PDB
- 3AQA
- Type
- protein
- Length
- 333 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2
- UniProt
- P25440
- Ligands
- BYH
- Pockets
- 7 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 2 | protein | 114 | 62% helix, 0% strand | P25440 |
| B | Bromodomain-containing protein 2 | protein | 112 | 63% helix, 0% strand | P25440 |
| C | Bromodomain-containing protein 2 | protein | 107 | 61% helix, 0% strand | P25440 |
Ligands and binding sites
- BYH · 1-[2-(1H-benzimidazol-2-ylsulfanyl)ethyl]-3-methyl-1,3-dihydro-2H-benzimidazole-2-thione · ligand · chains A
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 182 | 0.70 | 0.88 | 31 | empty |
| 2 | 130 | 0.54 | 0.81 | 18 | BYH |
| 3 | 122 | 0.50 | 0.80 | 19 | empty |
| 4 | 96 | 0.44 | 0.79 | 20 | empty |
| 5 | 67 | 0.38 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1084 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 530 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 47 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 modified (engineered).
Compared structures
- 3AQA · Crystal structure of the human BRD2 BD1 bromodomain in complex with a BRD2-interactive… · 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 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 P25440
- Elsewhere: RCSB PDB 3AQA · PDBe 3AQA · UniProt P25440
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