Research workbench
Structure of the kinase domain of human DDR1 in complex with a potent and selective inhibitor of DDR1 and DDR2
Analyse Structure of the kinase domain of human DDR1 in complex with a potent and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GWR
- Type
- protein
- Length
- 585 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
- FEW, SO4
- Pockets
- 7 · best druggability 0.83
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 | 300 | 41% helix, 18% strand | Q08345 |
| B | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 285 | 41% helix, 19% strand | Q08345 |
Ligands and binding sites
- FEW · 3-(2-imidazo[1,2-a]pyrazin-3-ylethynyl)-~{N}-[3-[(4-methylpiperazin-1-yl)methyl]-5-(trifluoromethyl) phenyl]-4-propan-2-yl-benzamide · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1086 | 0.83 | 0.84 | 87 | EDO, FEW |
| 2 | 786 | 0.74 | 0.78 | 59 | FEW, EDO |
| 3 | 226 | 0.54 | 0.77 | 27 | empty |
| 4 | 129 | 0.48 | 0.79 | 21 | EDO |
| 5 | 154 | 0.42 | 0.74 | 22 | empty |
Interfaces
1 interface between chains.
- A–B · 985 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 6GWR · Structure of the kinase domain of human DDR1 in complex with a potent and selective… · 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 0.97
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 6GWR · PDBe 6GWR · UniProt Q08345
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.