Research workbench
Non-oxime pyrazole based inhibitors of B-RAF kinase
Analyse Non-oxime pyrazole based inhibitors of B-RAF kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PSD
- Type
- protein
- Length
- 526 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B-RAF proto-oncogene SERINE/THREONINE-protein kinase
- EC
- 2.7.11.1
- UniProt
- P15056
- Ligands
- SM7
- Pockets
- 4 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | B-RAF proto-oncogene SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 262 | 38% helix, 17% strand | P15056 |
| B | B-RAF proto-oncogene SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 264 | 38% helix, 17% strand | P15056 |
Ligands and binding sites
- SM7 · 6-[1-(piperidin-4-yl)-3-(pyridin-4-yl)-1H-pyrazol-4-yl]indeno[1,2-c]pyrazole · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 301 | 0.71 | 0.85 | 50 | SM7 |
| 2 | 411 | 0.70 | 0.81 | 51 | empty |
| 3 | 227 | 0.68 | 0.85 | 31 | SM7 |
| 4 | 51 | 0.32 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1297 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 3PSD · Non-oxime pyrazole based inhibitors of B-Raf kinase · 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 3PSD · PDBe 3PSD · UniProt P15056
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