MolNFT v1 · #115093 · protein
Crystal structure of BRAF(V600E) in complex with LY3009120 compnd
5C9C · SERINE/THREONINE-protein kinase B-RAF: “Crystal structure of BRAF(V600E) in complex with LY3009120 compnd”. X-ray diffraction, 2 ligands (4Z5, CL), 3 pockets (best druggability 0.75). MolNFT v1 #115093 on GenesisL1: 3D structure…
- PDB
- 5C9C
- Type
- protein
- Length
- 505 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
- 4Z5, CL
- Pockets
- 3 · best druggability 0.75
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 | 41% helix, 18% strand | P15056 |
| B | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 251 | 41% helix, 18% strand | P15056 |
Ligands and binding sites
- 4Z5 · 1-(3,3-dimethylbutyl)-3-{2-fluoro-4-methyl-5-[7-methyl-2-(methylamino)pyrido[2,3-d]pyrimidin-6-yl]phenyl}urea · ligand · 2 copies · chains A, B
- CL · Chloride ion · ion · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 378 | 0.75 | 0.86 | 48 | empty |
| 2 | 454 | 0.72 | 0.82 | 47 | 4Z5 |
| 3 | 484 | 0.71 | 0.81 | 48 | 4Z5 |
Interfaces
1 interface between chains.
- A–B · 1163 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 5C9C · Crystal structure of BRAF(V600E) in complex with LY3009120 compnd · 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 5C9C · PDBe 5C9C · UniProt P15056
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