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Crystal structure of braf (R509H) kinase domain bound to AZ628
Analyse Crystal structure of braf (R509H) kinase domain bound to AZ628 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RZW
- Type
- protein
- Length
- 503 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
- B1E
- Pockets
- 5 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 251 | 41% helix, 17% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 252 | 39% helix, 15% strand | P15056 |
Ligands and binding sites
- B1E · 3-(2-cyanopropan-2-yl)-N-{4-methyl-3-[(3-methyl-4-oxo-3,4-dihydroquinazolin-6-yl)amino]phenyl}benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 409 | 0.71 | 0.82 | 37 | B1E |
| 2 | 423 | 0.70 | 0.81 | 45 | B1E |
| 3 | 54 | 0.64 | 0.94 | 22 | empty |
| 4 | 95 | 0.59 | 0.87 | 20 | empty |
| 5 | 111 | 0.56 | 0.84 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1354 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4RZW · Crystal structure of BRAF (R509H) kinase domain bound to AZ628 · 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 0.94
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 4RZW · PDBe 4RZW · UniProt P15056
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