Research workbench
Structure of the DDR1 kinase domain in complex with ponatinib
Analyse Structure of the DDR1 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
- 3ZOS
- Type
- protein
- Length
- 604 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epithelial discoidin domain-containing receptor 1
- EC
- 2.7.10.1
- UniProt
- Q08345
- Ligands
- 0LI
- Pockets
- 5 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 301 | 41% helix, 18% strand | Q08345 |
| B | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 303 | 41% helix, 18% strand | Q08345 |
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 · 3 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.85 | 0.87 | 100 | 0LI |
| 2 | 382 | 0.78 | 0.88 | 42 | 0LI |
| 3 | 110 | 0.77 | 0.97 | 23 | EDO |
| 4 | 179 | 0.46 | 0.75 | 31 | empty |
| 5 | 109 | 0.39 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1531 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- 3ZOS · Structure of the DDR1 kinase domain in complex with ponatinib · the same entry in another collection · chain A against A, TM-score 1.00
- Q08345 · AlphaFold monomer V2.0 prediction for epithelial discoidin domain- containing receptor 1… · a predicted model of the same protein · chain B 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 Q08345
- Elsewhere: RCSB PDB 3ZOS · PDBe 3ZOS · UniProt Q08345
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