MolNFT v1 · #133795 · protein
DDR1, N-[[2-(2-pyridin-3-YLOXYETHYL)CYCLOHEXYL]METHYL]-3- (TRIFLUOROMETHOXY)BENZAMIDE, 1.970A, P212121, RFREE=25.6%
5SB0 · Epithelial discoidin domain-containing receptor 1: “DDR1, N-[[2-(2-pyridin-3-YLOXYETHYL)CYCLOHEXYL]METHYL]-3- (TRIFLUOROMETHOXY)BENZAMIDE, 1.970A, P212121…”. X-ray diffraction, 3 ligands (1IZ, IOD, CL), 2 pockets (best druggability…
- PDB
- 5SB0
- Type
- protein
- Length
- 284 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
- 1IZ, IOD, CL
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 284 | 42% helix, 17% strand | Q08345 |
Ligands and binding sites
- 1IZ · N-{[(1R,2S)-2-{2-[(pyridin-3-yl) oxy]ethyl}cyclohexyl]methyl}-3-(trifluoromethoxy) benzamide · ligand · chains A
- IOD · Iodide ion · ion · chains A
- CL · Chloride 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 | 557 | 0.75 | 0.82 | 55 | 1IZ, CL |
| 2 | 59 | 0.35 | 0.77 | 11 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5SB0 · DDR1, N-[[2-(2-pyridin-3-yloxyethyl)cyclohexyl]methyl]-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 5SB0 · PDBe 5SB0 · UniProt Q08345
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