MolNFT v1 · #176522 · protein
Crystal structure of BRD2(BD1)WITH ligand zb-bd-224 bound
7DPN · Bromodomain-containing protein 2: “Crystal structure of BRD2(BD1)WITH ligand zb-bd-224 bound”. X-ray diffraction, 1 ligand (HFU), 5 pockets (best druggability 0.73). MolNFT v1 #176522 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7DPN
- Type
- protein
- Length
- 327 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bromodomain-containing protein 2
- UniProt
- P25440
- Ligands
- HFU
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 64% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bromodomain-containing protein 2 | protein | 114 | 61% helix, 2% strand | P25440 |
| B | Bromodomain-containing protein 2 | protein | 107 | 66% helix, 0% strand | P25440 |
| C | Bromodomain-containing protein 2 | protein | 106 | 64% helix, 0% strand | P25440 |
Ligands and binding sites
- HFU · 5-(1-naphthoyl)-11-methyl-8-((methylsulfonyl)methyl)-4, 5-dihydro-2,3A1,5-triazadibenzo[cd,h]azulen-1(2H)-one · ligand · 2 copies · chains A, B
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 | 351 | 0.73 | 0.84 | 52 | empty |
| 2 | 98 | 0.50 | 0.82 | 18 | HFU |
| 3 | 112 | 0.49 | 0.80 | 21 | HFU |
| 4 | 76 | 0.39 | 0.78 | 16 | empty |
| 5 | 69 | 0.37 | 0.78 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1099 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 454 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 43 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7DPN · Crystal structure of BRD2(BD1)with ligand ZB-BD-224 bound · 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 7DPN · PDBe 7DPN · UniProt P25440
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