MolNFT v1 · #120517 · protein
Crystal structure of PTK6 kinase domain complexed with dasatinib
5H2U · Protein-tyrosine kinase 6: “Crystal structure of PTK6 kinase domain complexed with dasatinib”. X-ray diffraction, 1 ligand (1N1), 11 pockets (best druggability 0.73). MolNFT v1 #120517 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5H2U
- Type
- protein
- Length
- 1,059 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein-tyrosine kinase 6
- EC
- 2.7.10.2
- UniProt
- Q13882
- Ligands
- 1N1
- Pockets
- 11 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Protein-tyrosine kinase 6 (EC 2.7.10.2) | protein | 266 | 44% helix, 18% strand | Q13882 |
| B, D | Protein-tyrosine kinase 6 (EC 2.7.10.2) | protein | 264 | 46% helix, 18% strand | Q13882 |
| C | Protein-tyrosine kinase 6 (EC 2.7.10.2) | protein | 265 | 45% helix, 18% strand | Q13882 |
Ligands and binding sites
- 1N1 · N-(2-chloro-6-methylphenyl)-2-({6-[4-(2-hydroxyethyl)piperazin-1-yl]-2-methylpyrimidin-4-yl}amino)-1,3-thiazole-5-carboxamide · ligand · 4 copies · chains A, B, C, D
- GOL · Glycerol · additive · 12 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 359 | 0.73 | 0.84 | 50 | 1N1, GOL |
| 2 | 328 | 0.72 | 0.85 | 46 | 1N1, GOL |
| 3 | 308 | 0.71 | 0.85 | 40 | GOL, 1N1 |
| 4 | 282 | 0.70 | 0.84 | 38 | 1N1, GOL |
| 5 | 648 | 0.68 | 0.77 | 46 | empty |
Interfaces
3 interfaces between chains.
- B–C · 819 Ų buried · 15 hydrogen bonds · protein-protein
- B–D · 348 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 224 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (carboxylation).
Compared structures
- 5H2U · Crystal structure of PTK6 Kinase Domain complexed with Dasatinib · the same entry in another collection · chain A against A, TM-score 1.00
- Q13882 · AlphaFold monomer V2.0 prediction for protein-tyrosine kinase 6 (Q13882) · a predicted model of the same protein · chain B against A, TM-score 0.89
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 Q13882
- Elsewhere: RCSB PDB 5H2U · PDBe 5H2U · UniProt Q13882
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