MolNFT v1 · #113172 · protein
Crystal structure of the second bromodomain of human BRD3 in complex with compound
5A7C · Bromodomain-containing protein 3: “Crystal structure of the second bromodomain of human BRD3 in complex with compound”. X-ray diffraction, 1 ligand (5D4), 6 pockets (best druggability 0.74). MolNFT v1 #113172 on GenesisL1: 3D…
- PDB
- 5A7C
- Type
- protein
- Length
- 441 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 3
- UniProt
- Q15059
- Ligands
- 5D4
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 3 | protein | 112 | 68% helix, 0% strand | Q15059 |
| B | Bromodomain-containing protein 3 | protein | 111 | 68% helix, 0% strand | Q15059 |
| C, D | Bromodomain-containing protein 3 | protein | 109 | 70% helix, 0% strand | Q15059 |
Ligands and binding sites
- 5D4 · N-(6-acetamidohexyl)acetamide · ligand · 4 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 718 | 0.74 | 0.80 | 60 | 5D4, EDO |
| 2 | 362 | 0.58 | 0.76 | 35 | empty |
| 3 | 374 | 0.57 | 0.75 | 36 | empty |
| 4 | 111 | 0.48 | 0.80 | 21 | 5D4 |
| 5 | 114 | 0.48 | 0.79 | 21 | 5D4 |
Interfaces
4 interfaces between chains.
- A–B · 755 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 741 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 521 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 72 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5A7C · Crystal structure of the second bromodomain of human BRD3 in complex with compound · the same entry in another collection · chain D against D, TM-score 1.00
- Q15059 · AlphaFold monomer V2.0 prediction for bromodomain-containing protein 3 (Q15059) · a predicted model of the same protein · chain C 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 Q15059
- Elsewhere: RCSB PDB 5A7C · PDBe 5A7C · UniProt Q15059
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