MolNFT v1 · #117029 · protein
X-ray crystal structure of human BRD2(BD2) in complex with RVX297 to 1.55 a resolution
5DW1 · Bromodomain-containing protein 2: “X-ray crystal structure of human BRD2(BD2) in complex with RVX297 to 1.55 a resolution”. X-ray diffraction, 2 ligands (5GD, NA), 5 pockets (best druggability 0.85). MolNFT v1 #117029 on GenesisL1…
- PDB
- 5DW1
- Type
- protein
- Length
- 441 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2
- UniProt
- P25440
- Ligands
- 5GD, NA
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 2 | protein | 111 | 68% helix, 0% strand | P25440 |
| B, C, D | Bromodomain-containing protein 2 | protein | 110 | 69% helix, 0% strand | P25440 |
Ligands and binding sites
- 5GD · 2-{3,5-dimethyl-4-[2-(pyrrolidin-1-yl)ethoxy]phenyl}-5,7-dimethoxyquinazolin-4(3H)-one · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1159 | 0.85 | 0.86 | 87 | empty |
| 2 | 105 | 0.52 | 0.82 | 19 | 5GD |
| 3 | 114 | 0.50 | 0.80 | 20 | 5GD |
| 4 | 114 | 0.48 | 0.79 | 20 | 5GD |
| 5 | 102 | 0.48 | 0.80 | 19 | 5GD |
Interfaces
6 interfaces between chains.
- C–D · 862 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 840 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 476 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 461 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 40 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5DW1 · X-ray crystal structure of human BRD2(BD2) in complex with RVX297 to 1.55 A resolution · the same entry in another collection · chain D against D, 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 5DW1 · PDBe 5DW1 · UniProt P25440
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