MolNFT v1 · #176449 · protein
The crystal structure of CPD8 in complex with bptf bromodomain
7DN4 · Nucleosome-remodeling factor subunit bptf: “The crystal structure of CPD8 in complex with bptf bromodomain”. X-ray diffraction, 1 ligand (JC3), 20 pockets (best druggability 0.54). MolNFT v1 #176449 on GenesisL1: 3D structure…
- PDB
- 7DN4
- Type
- protein
- Length
- 708 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleosome-remodeling factor subunit bptf
- UniProt
- Q12830
- Ligands
- JC3
- Pockets
- 20 · best druggability 0.54
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Nucleosome-remodeling factor subunit bptf | protein | 118 | 66% helix, 0% strand | Q12830 |
Ligands and binding sites
- JC3 · 3-methyl-2-[[(3R,5R)-1-methyl-5-phenyl-piperidin-3-yl]amino]-6,7-dihydro-5H-cyclopenta[d]pyrimidin-4-one · ligand · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 150 | 0.54 | 0.80 | 21 | JC3 |
| 2 | 150 | 0.53 | 0.80 | 26 | JC3 |
| 3 | 109 | 0.49 | 0.80 | 20 | JC3 |
| 4 | 97 | 0.48 | 0.81 | 17 | JC3 |
| 5 | 116 | 0.47 | 0.79 | 18 | empty |
Interfaces
7 interfaces between chains.
- B–E · 472 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 453 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 436 Ų buried · 9 hydrogen bonds · protein-protein
- E–F · 306 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 303 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7DN4 · The crystal structure of Cpd8 in complex with BPTF bromodomain · the same entry in another collection · chain A against A, TM-score 1.00
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 Q12830
- Elsewhere: RCSB PDB 7DN4 · PDBe 7DN4 · UniProt Q12830
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