MolNFT v1 · #85349 · protein
N-terminal bromodomain of human BRD2 with N-cyclopropyl-5-(3,5- dimethyl-1,2-oxazol-4-yl)-2-methylbenzene-1-sulfonamide
4A9N · Bromodomain containing 2: “N-terminal bromodomain of human BRD2 with N-cyclopropyl-5-(3,5…”. X-ray diffraction, 2 ligands (A9N, SO4), 6 pockets (best druggability 0.72). MolNFT v1 #85349 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4A9N
- Type
- protein
- Length
- 333 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain containing 2
- UniProt
- P25440
- Ligands
- A9N, SO4
- Pockets
- 6 · best druggability 0.72
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 | 115 | 61% helix, 0% strand | P25440 |
| C | Bromodomain containing 2 | protein | 106 | 62% helix, 0% strand | P25440 |
Ligands and binding sites
- A9N · N-cycloprop-2-en-1-yl-5-(3,5-dimethyl-1,2-oxazol-4-yl)-2-methyl-benzenesulfonamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C
- DMS · Dimethyl sulfoxide · additive · chains C
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 | 457 | 0.72 | 0.82 | 43 | DMS |
| 2 | 112 | 0.52 | 0.81 | 19 | A9N |
| 3 | 132 | 0.52 | 0.80 | 21 | A9N |
| 4 | 69 | 0.39 | 0.79 | 19 | EDO |
| 5 | 87 | 0.35 | 0.75 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1096 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 356 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 124 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4A9N · N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH N-cyclopropyl-5-(3,5… · 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 4A9N · PDBe 4A9N · UniProt P25440
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