MolNFT v1 · #133792 · protein
DDR1, 2-[3-(2-pyridin-3-YLETHYNYL)PHENYL]-N-[3-(trifluoromethyl) PHENYL]ACETAMIDE, 1.902A, second P212121 form, RFREE=25.4%, second form
5SAX · Epithelial discoidin domain-containing receptor 1: “DDR1, 2-[3-(2-pyridin-3-YLETHYNYL)PHENYL]-N-[3-(trifluoromethyl) PHENYL]ACETAMIDE, 1.902A, second P212121…”. X-ray diffraction, 2 ligands (1IM, IOD), 2 pockets (best druggability…
- PDB
- 5SAX
- Type
- protein
- Length
- 302 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
- 1IM, IOD
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 302 | 40% helix, 16% strand | Q08345 |
Ligands and binding sites
- 1IM · 2-{3-[(pyridin-3-yl)ethynyl]phenyl}-N-[3-(trifluoromethyl)phenyl]acetamide · ligand · chains A
- IOD · Iodide ion · ion · 8 copies · 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 | 477 | 0.75 | 0.83 | 54 | IOD, 1IM |
| 2 | 63 | 0.31 | 0.75 | 16 | empty |
Compared structures
- 5SAX · DDR1, 2-[3-(2-pyridin-3-ylethynyl)phenyl]-N-[3-(trifluoromethyl)phenyl]acetamide, 1.902A… · 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 5SAX · PDBe 5SAX · UniProt Q08345
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