Research workbench
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 v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- 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 · 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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