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 v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.5
- Source
- Homo sapiens
- 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 · resolution 3.5 · 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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