Research workbench
Structure of the B-RAF kinase domain bound to sb-590885
Analyse Structure of the B-RAF kinase domain bound to sb-590885 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2FB8
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-RAF proto-oncogene SERINE/THREONINE-protein kinase
- EC
- 2.7.1.37
- UniProt
- P15056
- Ligands
- 215
- Pockets
- 5 · best druggability 0.69
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | B-RAF proto-oncogene SERINE/THREONINE-protein kinase (EC 2.7.1.37) | protein | 259 | 39% helix, 17% strand | P15056 |
Ligands and binding sites
- 215 · (1Z)-5-(2-{4-[2-(dimethylamino)ethoxy]phenyl}-5-pyridin-4-yl-1H-imidazol-4-yl)indan-1-one oxime · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 254 | 0.69 | 0.84 | 31 | 215 |
| 2 | 262 | 0.67 | 0.83 | 32 | 215 |
| 3 | 72 | 0.65 | 0.93 | 29 | empty |
| 4 | 176 | 0.58 | 0.81 | 24 | empty |
| 5 | 138 | 0.51 | 0.80 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1101 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 2FB8 · Structure of the B-Raf kinase domain bound to SB-590885 · the same entry in another collection · chain A against A, TM-score 1.00
- 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 0.95
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 2FB8 · PDBe 2FB8 · UniProt P15056
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