Research workbench
DDR1, N-[2-[3-(2-aminopyrimidin-5-YL)OXYPHENYL]ETHYL]-3- (TRIFLUOROMETHOXY)BENZAMIDE, 2.190A, P1211, RFREE=27.7%
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
- 5SAY
- Type
- protein
- Length
- 578 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
- 1IJ, IOD
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 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 | 290 | 39% helix, 17% strand | Q08345 |
| B | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 288 | 42% helix, 17% strand | Q08345 |
Ligands and binding sites
- 1IJ · N-(2-{3-[(2-aminopyrimidin-5-yl)oxy]phenyl}ethyl)-3-(trifluoromethoxy)benzamide · ligand · 2 copies · chains A, B
- IOD · Iodide ion · ion · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1188 | 0.83 | 0.84 | 95 | IOD, 1IJ |
| 2 | 548 | 0.75 | 0.82 | 53 | IOD, 1IJ |
| 3 | 200 | 0.51 | 0.77 | 32 | empty |
| 4 | 98 | 0.38 | 0.75 | 23 | empty |
Interfaces
1 interface between chains.
- A–B · 1134 Ų buried · 15 hydrogen bonds · protein-protein
Compared structures
- 5SAY · 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 0.97
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 5SAY · PDBe 5SAY · UniProt Q08345
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.