Research workbench
The complex structure of braf V600E kinase domain with a novel braf inhibitor
Analyse The complex structure of braf V600E kinase domain with a novel braf inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R5Y
- Type
- protein
- Length
- 507 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
- 3K3
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 253 | 42% helix, 18% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 254 | 39% helix, 18% strand | P15056 |
Ligands and binding sites
- 3K3 · 5-({(1R,1aS,6bR)-1-[5-(trifluoromethyl)-1H-benzimidazol-2-yl]-1a,6b-dihydro-1H-cyclopropa[b][1]benzofuran-5-yl}oxy)-3,4-dihydro-1,8-naphthyridin-2(1H)-one · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 557 | 0.71 | 0.80 | 51 | 3K3 |
| 2 | 330 | 0.67 | 0.81 | 37 | 3K3 |
| 3 | 63 | 0.66 | 0.95 | 23 | empty |
| 4 | 173 | 0.54 | 0.80 | 18 | empty |
| 5 | 214 | 0.53 | 0.78 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 1245 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 4R5Y · The complex structure of Braf V600E kinase domain with a novel Braf 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 0.95
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 4R5Y · PDBe 4R5Y · UniProt P15056
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