Research workbench
Human B-RAF kinase domain bound to a type II pyrazolopyridine inhibitor
Analyse Human B-RAF kinase domain bound to a type II pyrazolopyridine inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4G9C
- Type
- protein
- Length
- 529 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
- 0WP
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 265 | 38% helix, 15% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 264 | 38% helix, 16% strand | P15056 |
Ligands and binding sites
- 0WP · 3-{[3-(2-cyanopropan-2-yl)benzoyl]amino}-2,6-difluoro-N-(3-methoxy-2H-pyrazolo[3,4-b]pyridin-5-yl)benzamide · 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 | 666 | 0.77 | 0.82 | 63 | 0WP |
| 2 | 321 | 0.70 | 0.83 | 39 | 0WP |
| 3 | 88 | 0.61 | 0.89 | 26 | empty |
| 4 | 186 | 0.56 | 0.81 | 20 | empty |
| 5 | 182 | 0.55 | 0.80 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 1243 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 4G9C · Human B-Raf Kinase Domain bound to a Type II Pyrazolopyridine 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 B 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 4G9C · PDBe 4G9C · UniProt P15056
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