Research workbench
Fragment-based discovery of potent and selective DDR1/2 inhibitors
Analyse Fragment-based discovery of potent and selective DDR1/2 inhibitors in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BVN
- Type
- protein
- Length
- 278 residues
- Chains
- 1
- 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
- 4VD, IOD
- Pockets
- 2 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 278 | 41% helix, 17% strand | Q08345 |
Ligands and binding sites
- 4VD · N-[5-({[(3-fluorophenyl)carbamoyl]amino}methyl)-2-methylphenyl]imidazo[1,2-a]pyridine-3-carboxamide · ligand · chains A
- IOD · Iodide ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.72 | 0.82 | 48 | 4VD |
| 2 | 51 | 0.32 | 0.76 | 11 | empty |
Compared structures
- 5BVN · Fragment-based discovery of potent and selective DDR1/2 inhibitors · 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 0.97
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 5BVN · PDBe 5BVN · UniProt Q08345
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