Research workbench
Crystal structure of RAF kinase domain bound to the inhibitor 2A
Analyse Crystal structure of RAF kinase domain bound to the inhibitor 2A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CAD
- Type
- protein
- Length
- 497 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- SERINE/THREONINE-protein kinase B-RAF
- EC
- 2.7.11.1
- UniProt
- P15056
- Ligands
- EU4
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 249 | 43% helix, 17% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 248 | 41% helix, 17% strand | P15056 |
Ligands and binding sites
- EU4 · 1-(propan-2-yl)-3-({3-[3-(trifluoromethyl) phenyl]isoquinolin-8-yl}ethynyl)-1H-pyrazolo[3,4-d]pyrimidin-4-amine · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 496 | 0.72 | 0.81 | 48 | EU4 |
| 2 | 84 | 0.69 | 0.94 | 23 | empty |
| 3 | 379 | 0.68 | 0.81 | 39 | EU4 |
| 4 | 142 | 0.51 | 0.80 | 15 | empty |
| 5 | 133 | 0.49 | 0.79 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 1172 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 6CAD · Crystal structure of RAF kinase domain bound to the inhibitor 2a · 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 B against A, TM-score 0.96
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 6CAD · PDBe 6CAD · UniProt P15056
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