Research workbench
Crystal structure of braf kinase domain bound to az-vem
Analyse Crystal structure of braf kinase domain bound to az-vem in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5ITA
- Type
- protein
- Length
- 502 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
- 6DC
- Pockets
- 6 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 250 | 43% helix, 18% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 252 | 41% helix, 16% strand | P15056 |
Ligands and binding sites
- 6DC · N-{2-cyano-3-[(3-methyl-4-oxo-3,4-dihydroquinazolin-6-yl)amino]phenyl}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
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 249 | 0.70 | 0.85 | 34 | 6DC |
| 2 | 253 | 0.64 | 0.82 | 33 | 6DC |
| 3 | 54 | 0.53 | 0.89 | 18 | empty |
| 4 | 67 | 0.49 | 0.85 | 18 | empty |
| 5 | 50 | 0.35 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1341 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 5ITA · Crystal Structure of BRAF Kinase Domain Bound to AZ-VEM · 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 0.98
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 5ITA · PDBe 5ITA · UniProt P15056
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