Research workbench
B-RAF kinase domain in complex with an aminopyridimine-based inhibitor
Analyse B-RAF kinase domain in complex with an aminopyridimine-based inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EHG
- Type
- protein
- Length
- 522 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
- RI9
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 262 | 38% helix, 17% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 260 | 39% helix, 14% strand | P15056 |
Ligands and binding sites
- RI9 · N-{2,4-difluoro-3-[({6-[(2-hydroxyethyl)amino]pyrimidin-4-yl}carbamoyl)amino]phenyl}propane-1-sulfonamide · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 414 | 0.75 | 0.84 | 56 | RI9 |
| 2 | 383 | 0.70 | 0.82 | 47 | RI9 |
| 3 | 70 | 0.66 | 0.94 | 25 | empty |
| 4 | 192 | 0.56 | 0.80 | 24 | empty |
| 5 | 195 | 0.56 | 0.80 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 1141 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4EHG · B-Raf Kinase Domain in Complex with an Aminopyridimine-based Inhibitor · 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 0.98
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 4EHG · PDBe 4EHG · UniProt P15056
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