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Crystal structure of the BRAF (R509H) kinase domain monomer bound to Vemurafenib
Analyse Crystal structure of the BRAF (R509H) kinase domain monomer bound to Vemurafenib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RZV
- Type
- protein
- Length
- 532 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.994
- Source
- Homo sapiens
- Molecule
- Serine/threonine-protein kinase B-raf
- EC
- 2.7.11.1
- UniProt
- P15056
- Ligands
- 032
- Pockets
- 9 · best druggability 0.76
Structure
x-ray diffraction · resolution 2.994 · 2 distinct chains · 40% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Serine/threonine-protein kinase B-raf (EC 2.7.11.1) | protein | 261 | 38% helix, 15% strand | P15056 |
| B | Serine/threonine-protein kinase B-raf (EC 2.7.11.1) | protein | 271 | 42% helix, 15% strand | P15056 |
Ligands and binding sites
- 032 · N-(3-{[5-(4-chlorophenyl)-1H-pyrrolo[2,3-b]pyridin-3-yl]carbonyl}-2,4-difluorophenyl)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
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.76 | 0.86 | 55 | 032 |
| 2 | 441 | 0.75 | 0.84 | 56 | 032 |
| 3 | 396 | 0.63 | 0.77 | 47 | empty |
| 4 | 70 | 0.46 | 0.82 | 24 | empty |
| 5 | 146 | 0.44 | 0.76 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 906 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4RZV · Crystal structure of the braf (R509H) kinase domain monomer bound to vemurafenib · 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 4RZV · PDBe 4RZV · UniProt P15056
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