MolNFT v1 · #85343 · protein
N-terminal bromodomain of human BRD2 with 1-(2-methyl-1,2,3,4- tetrahydroquinolin-1-YL)ETHAN-1-one
4A9H · Bromodomain-containing protein 2: “N-terminal bromodomain of human BRD2 with 1-(2-methyl-1,2,3,4- tetrahydroquinolin-1-YL)ETHAN-1-one”. X-ray diffraction, 2 ligands (TVP, SO4), 6 pockets (best druggability 0.75). MolNFT v1 #85343 on…
- PDB
- 4A9H
- Type
- protein
- Length
- 326 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2
- UniProt
- P25440
- Ligands
- TVP, SO4
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 2 | protein | 112 | 63% helix, 0% strand | P25440 |
| B, C | Bromodomain-containing protein 2 | protein | 107 | 67% helix, 0% strand | P25440 |
Ligands and binding sites
- TVP · (2S)-1-acetyl-2-methyl-1,2,3,4-tetrahydroquinoline · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
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 | 308 | 0.75 | 0.87 | 32 | TVP |
| 2 | 112 | 0.51 | 0.81 | 19 | TVP |
| 3 | 117 | 0.50 | 0.80 | 21 | EDO, TVP |
| 4 | 79 | 0.37 | 0.77 | 18 | empty |
| 5 | 90 | 0.36 | 0.75 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1080 Ų buried · 13 hydrogen bonds · protein-protein
- A–C · 490 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 95 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4A9H · N-TERMINAL BROMODOMAIN OF HUMAN BRD2 WITH 1-(2-methyl-1,2,3,4-tetrahydroquinolin-1-yl)etha… · 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 4A9H · PDBe 4A9H · UniProt P25440
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