Research workbench
The complex of wild-type B-RAF with pyrazolo pyrimidine inhibitor
Analyse The complex of wild-type B-RAF with pyrazolo pyrimidine inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3II5
- Type
- protein
- Length
- 519 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
- 831, PO4
- Pockets
- 4 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 41% 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 | 40% helix, 17% strand | P15056 |
| B | B-RAF proto-oncogene SERINE/THREONINE-protein kinase (EC 2.7.11.1) | protein | 257 | 41% helix, 18% strand | P15056 |
Ligands and binding sites
- 831 · N-[3-(3-{4-[(dimethylamino)methyl]phenyl}pyrazolo[1,5-a]pyrimidin-7-yl)phenyl]-3-(trifluoromethyl)benzamide · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.75 | 0.80 | 65 | 831 |
| 2 | 504 | 0.72 | 0.81 | 50 | 831 |
| 3 | 234 | 0.66 | 0.84 | 36 | PO4 |
| 4 | 129 | 0.55 | 0.83 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 1236 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 3II5 · The Complex of wild-type B-RAF with Pyrazolo pyrimidine 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 3II5 · PDBe 3II5 · UniProt P15056
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