Research workbench
Crystal structure of braf kinase domain bound to the inhibitor 2L
Analyse Crystal structure of braf kinase domain bound to the inhibitor 2L in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6NSQ
- Type
- protein
- Length
- 527 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
- KZP
- Pockets
- 8 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 253 | 42% helix, 17% strand | P15056 |
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 274 | 41% helix, 16% strand | P15056 |
Ligands and binding sites
- KZP · 5-[(4-amino-1-ethyl-1H-pyrazolo[3,4-d]pyrimidin-3-yl) ethynyl]-N-(4-chlorophenyl)-6-methylisoquinolin-1-amine · ligand · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 563 | 0.74 | 0.81 | 56 | KZP |
| 2 | 402 | 0.73 | 0.83 | 39 | KZP |
| 3 | 53 | 0.60 | 0.92 | 19 | empty |
| 4 | 148 | 0.56 | 0.82 | 21 | empty |
| 5 | 136 | 0.56 | 0.83 | 17 | empty |
Interfaces
1 interface between chains.
- B–A · 1244 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 6NSQ · Crystal structure of BRAF kinase domain bound to the inhibitor 2l · the same entry in another collection · chain B against B, 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 6NSQ · PDBe 6NSQ · UniProt P15056
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