Research workbench
Crystal structure of the human DDR1 kinase domain in complex with imatinib
Analyse Crystal structure of the human DDR1 kinase domain in complex with imatinib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BKJ
- Type
- protein
- Length
- 592 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
- STI
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 295 | 43% helix, 17% strand | Q08345 |
| B | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 297 | 42% helix, 16% strand | Q08345 |
Ligands and binding sites
- STI · 4-(4-methyl-piperazin-1-ylmethyl)-N-[4-methyl-3-(4-pyridin-3-yl-pyrimidin-2-ylamino)-phenyl]-benzamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 19 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 630 | 0.75 | 0.81 | 56 | EDO, STI |
| 2 | 636 | 0.75 | 0.81 | 57 | STI |
| 3 | 146 | 0.51 | 0.79 | 28 | empty |
| 4 | 117 | 0.37 | 0.74 | 17 | empty |
| 5 | 63 | 0.33 | 0.76 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 320 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 4BKJ · Crystal structure of the human DDR1 kinase domain in complex with imatinib · 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 A against A, TM-score 0.95
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 4BKJ · PDBe 4BKJ · UniProt Q08345
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