Research workbench
DDR1, N-[2-[3-(2-aminopyrimidin-5-YL)OXYPHENYL]ETHYL]-3- (TRIFLUOROMETHOXY)BENZAMIDE, 1.760A, P212121, RFREE=23.5%
Analyse DDR1, N-[2-[3-(2-aminopyrimidin-5-YL)OXYPHENYL]ETHYL]-3… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SAV
- Type
- protein
- Length
- 291 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
- 1IJ, IOD
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 291 | 41% helix, 16% strand | Q08345 |
Ligands and binding sites
- 1IJ · N-(2-{3-[(2-aminopyrimidin-5-yl)oxy]phenyl}ethyl)-3-(trifluoromethoxy)benzamide · ligand · chains A
- IOD · Iodide ion · ion · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 674 | 0.72 | 0.79 | 54 | 1IJ |
Compared structures
- 5SAV · DDR1, N-[2-[3-(2-aminopyrimidin-5-yl)oxyphenyl]ethyl]-3-(trifluoromethoxy)benzamide… · 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 0.94
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 5SAV · PDBe 5SAV · UniProt Q08345
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