Research workbench
Human B-RAF kinase domain in complex with an imidazopyridine-based inhibitor
Analyse Human B-RAF kinase domain in complex with an imidazopyridine-based inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4MBJ
- Type
- protein
- Length
- 545 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
- DFS
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 36% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 269 | 36% helix, 13% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 276 | 36% helix, 12% strand | P15056 |
Ligands and binding sites
- DFS · 2,6-difluoro-N-(1H-imidazo[4,5-b]pyridin-6-yl)-3-[(propylsulfonyl)amino]benzamide · 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 617 | 0.77 | 0.83 | 66 | DFS |
| 2 | 365 | 0.71 | 0.83 | 34 | DFS |
| 3 | 177 | 0.61 | 0.83 | 33 | empty |
| 4 | 61 | 0.60 | 0.91 | 21 | empty |
| 5 | 190 | 0.54 | 0.79 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 1179 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4MBJ · Human B-Raf Kinase Domain in Complex with an Imidazopyridine-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 0.97
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 4MBJ · PDBe 4MBJ · UniProt P15056
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.