MolNFT v1 · #88983 · protein
Crystal structure of the kinase domain of human B-RAF with a [1, 3]THIAZOLO[5,4-B]PYRIDINE derivative
4DBN · SERINE/THREONINE-protein kinase B-RAF: “Crystal structure of the kinase domain of human B-RAF with a [1, 3]THIAZOLO[5,4-B]PYRIDINE derivative”. X-ray diffraction, 1 ligand (0JA), 5 pockets (best druggability 0.73). MolNFT v1 #88983…
- PDB
- 4DBN
- Type
- protein
- Length
- 520 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
- 0JA
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 257 | 42% helix, 17% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 263 | 41% helix, 14% strand | P15056 |
Ligands and binding sites
- 0JA · 2-chloro-3-(1-cyanocyclopropyl)-N-[5-({2-[(cyclopropylcarbonyl)amino][1,3]thiazolo[5,4-b]pyridin-5-yl}oxy)-2-fluorophenyl]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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 268 | 0.73 | 0.87 | 37 | 0JA |
| 2 | 454 | 0.71 | 0.81 | 48 | 0JA |
| 3 | 241 | 0.68 | 0.85 | 39 | empty |
| 4 | 120 | 0.57 | 0.85 | 17 | empty |
| 5 | 54 | 0.24 | 0.72 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 1224 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4DBN · Crystal Structure of the Kinase domain of Human B-raf with a [1,3]thiazolo[5,4-b]pyridine… · 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 4DBN · PDBe 4DBN · UniProt P15056
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