Research workbench
Src kinase domain in complex with ponatinib
Analyse Src kinase domain in complex with ponatinib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OTE
- Type
- protein
- Length
- 518 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Proto-oncogene tyrosine-protein kinase src
- EC
- 2.7.10.2
- UniProt
- P12931
- Ligands
- 0LI
- Pockets
- 4 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Proto-oncogene tyrosine-protein kinase src (EC 2.7.10.2) | protein | 259 | 42% helix, 16% strand | P12931 |
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 · 2 copies · chains A, B
- GOL · Glycerol · additive · 10 copies · chains A, B
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 710 | 0.77 | 0.82 | 84 | 0LI, GOL |
| 2 | 405 | 0.74 | 0.84 | 44 | 0LI |
| 3 | 260 | 0.59 | 0.79 | 44 | TRS, GOL |
| 4 | 104 | 0.36 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 400 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7OTE · Src Kinase Domain in complex with ponatinib · the same entry in another collection · chain A against A, TM-score 1.00
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 P12931
- Elsewhere: RCSB PDB 7OTE · PDBe 7OTE · UniProt P12931
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