Research workbench
BRAF kinase in complex with LXH254 (naporafenib)
Analyse BRAF kinase in complex with LXH254 (naporafenib) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8F7P
- Type
- protein
- Length
- 520 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.74
- Source
- Homo sapiens
- Molecule
- Serine/threonine-protein kinase B-raf
- EC
- 2.7.11.1
- UniProt
- P15056
- Ligands
- K81
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.74 · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine/threonine-protein kinase B-raf (EC 2.7.11.1) | protein | 255 | 41% helix, 18% strand | P15056 |
| B | Serine/threonine-protein kinase B-raf (EC 2.7.11.1) | protein | 265 | 39% helix, 16% strand | P15056 |
Ligands and binding sites
- K81 · N-{3-[2-(2-hydroxyethoxy)-6-(morpholin-4-yl)pyridin-4-yl]-4-methylphenyl}-2-(trifluoromethyl)pyridine-4-carboxamide · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.76 | 0.81 | 58 | K81 |
| 2 | 388 | 0.72 | 0.84 | 50 | empty |
| 3 | 568 | 0.72 | 0.80 | 49 | K81 |
| 4 | 52 | 0.42 | 0.83 | 15 | empty |
| 5 | 67 | 0.30 | 0.73 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 1244 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- P15056 · AlphaFold monomer V2.0 prediction for SERINE/THREONINE-protein kinase B-RAF (P15056) · a predicted model of the same protein · chain A against A, TM-score 0.94
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 P15056
- Elsewhere: RCSB PDB 8F7P · PDBe 8F7P · UniProt P15056
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