MolNFT v1 · #159855 · protein
The co-crystal structure of BRAF(V600E) with ponatinib
6P3D · SERINE/THREONINE-protein kinase B-RAF: “The co-crystal structure of BRAF(V600E) with ponatinib”. X-ray diffraction, 3 ligands (0LI, SO4, NH4), 2 pockets (best druggability 0.71). MolNFT v1 #159855 on GenesisL1: 3D structure, binding…
- PDB
- 6P3D
- Type
- protein
- Length
- 264 residues
- Chains
- 1
- 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
- 0LI, SO4, NH4
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | SERINE/THREONINE-protein kinase B-RAF (EC 2.7.11.1) | protein | 264 | 43% helix, 17% strand | P15056 |
Ligands and binding sites
- 0LI · 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl) phenyl}benzamide · ligand · chains A
- SO4 · Sulfate ion · ion · 8 copies · chains A
- NH4 · Ammonium ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 403 | 0.71 | 0.82 | 45 | 0LI |
| 2 | 71 | 0.46 | 0.82 | 22 | empty |
Compared structures
- 6P3D · The co-crystal structure of BRAF(V600E) with ponatinib · 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 0.94
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 6P3D · PDBe 6P3D · UniProt P15056
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