MolNFT v1 · #91394 · protein
Crystal structure of human kinase domain of B-RAF with a dfg-out inhibitor
4FC0 · SERINE/THREONINE-protein kinase B-RAF: “Crystal structure of human kinase domain of B-RAF with a dfg-out inhibitor”. X-ray diffraction, 1 ligand (0T2), 5 pockets (best druggability 0.74). MolNFT v1 #91394 on GenesisL1: 3D structure…
- PDB
- 4FC0
- Type
- protein
- Length
- 517 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
- 0T2
- Pockets
- 5 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 254 | 42% helix, 18% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 263 | 40% helix, 17% strand | P15056 |
Ligands and binding sites
- 0T2 · 2-chloro-3-[(2-cyanopropan-2-yl)oxy]-N-{5-[{2-[(cyclopropylcarbonyl)amino][1,3]thiazolo[5,4-b]pyridin-5-yl}(methyl)amino]-2-fluorophenyl}benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.74 | 0.84 | 50 | 0T2 |
| 2 | 470 | 0.69 | 0.80 | 45 | 0T2 |
| 3 | 70 | 0.68 | 0.95 | 25 | empty |
| 4 | 114 | 0.58 | 0.85 | 21 | empty |
| 5 | 205 | 0.56 | 0.79 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 1238 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 4FC0 · Crystal Structure of Human Kinase Domain of B-raf with a DFG-out 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 0.96
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 4FC0 · PDBe 4FC0 · UniProt P15056
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