Research workbench
B-RAF wild-type kinase domain in complex with a purinylpyridinylamino- based inhibitor
Analyse B-RAF wild-type kinase domain in complex with a purinylpyridinylamino- based… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FD2
- Type
- protein
- Length
- 498 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
- 5XJ
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 264 | 42% helix, 16% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 234 | 43% helix, 15% strand | P15056 |
Ligands and binding sites
- 5XJ · 6-[2-[[3-(dimethylsulfamoylamino)-2,6-bis(fluoranyl)phenyl]amino]pyridin-3-yl]-7~{H}-purine · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 488 | 0.73 | 0.82 | 55 | 5XJ |
| 2 | 286 | 0.60 | 0.79 | 37 | empty |
| 3 | 271 | 0.59 | 0.78 | 30 | 5XJ |
| 4 | 121 | 0.51 | 0.80 | 18 | empty |
| 5 | 70 | 0.43 | 0.81 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 472 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 5FD2 · B-Raf wild-type kinase domain in complex with a purinylpyridinylamino-based 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 0.98
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 5FD2 · PDBe 5FD2 · UniProt P15056
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