Research workbench
Human B-RAF kinase in complex with an amide linked pyrazolopyridine inhibitor
Analyse Human B-RAF kinase in complex with an amide linked pyrazolopyridine inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3SKC
- Type
- protein
- Length
- 536 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
- BR2
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 260 | 40% helix, 15% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 276 | 39% helix, 14% strand | P15056 |
Ligands and binding sites
- BR2 · 2,6-difluoro-N-[(5S)-3-methoxy-5H-pyrazolo[3,4-b]pyridin-5-yl]-3-[(phenylsulfonyl)amino]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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 690 | 0.78 | 0.83 | 72 | BR2 |
| 2 | 490 | 0.70 | 0.80 | 52 | BR2 |
| 3 | 91 | 0.68 | 0.93 | 29 | empty |
| 4 | 250 | 0.56 | 0.78 | 34 | empty |
| 5 | 202 | 0.56 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1172 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 3SKC · Human B-Raf Kinase in Complex with an Amide Linked 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 A against A, TM-score 0.98
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 3SKC · PDBe 3SKC · UniProt P15056
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