MolNFT v1 · #110385 · protein
B-RAF kinase V600E oncogenic mutant in complex with PLX7904
4XV1 · SERINE/THREONINE-protein kinase B-RAF: “B-RAF kinase V600E oncogenic mutant in complex with PLX7904”. X-ray diffraction, 1 ligand (904), 5 pockets (best druggability 0.67). MolNFT v1 #110385 on GenesisL1: 3D structure, binding sites…
- PDB
- 4XV1
- Type
- protein
- Length
- 488 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
- 904
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 239 | 41% helix, 17% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 249 | 43% helix, 16% strand | P15056 |
Ligands and binding sites
- 904 · N'-(3-{[5-(2-cyclopropylpyrimidin-5-yl)-1H-pyrrolo[2,3-b]pyridin-3-yl]carbonyl}-2,4-difluorophenyl)-N-ethyl-N-methylsulfuric diamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 256 | 0.67 | 0.83 | 34 | 904 |
| 2 | 182 | 0.64 | 0.84 | 27 | empty |
| 3 | 106 | 0.56 | 0.85 | 18 | empty |
| 4 | 105 | 0.55 | 0.85 | 17 | empty |
| 5 | 66 | 0.33 | 0.76 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1252 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 4XV1 · B-Raf Kinase V600E oncogenic mutant in complex with PLX7904 · 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 4XV1 · PDBe 4XV1 · UniProt P15056
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