MolNFT v1 · #114636 · protein
Fragment-based discovery of potent and selective DDR1/2 inhibitors
5BVK · Epithelial discoidin domain-containing receptor 1: “Fragment-based discovery of potent and selective DDR1/2 inhibitors”. X-ray diffraction, 2 ligands (4VC, IOD), 1 pocket (best druggability 0.74). MolNFT v1 #114636 on GenesisL1: 3D…
- PDB
- 5BVK
- 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
- 4VC, IOD
- Pockets
- 1 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epithelial discoidin domain-containing receptor 1 (EC 2.7.10.1) | protein | 278 | 42% helix, 18% strand | Q08345 |
Ligands and binding sites
- 4VC · 1-(2-chlorophenyl)-3-(pyridin-3-ylmethyl)urea · ligand · chains A
- IOD · Iodide ion · ion · 6 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 | 453 | 0.74 | 0.83 | 58 | IOD, 4VC |
Compared structures
- 5BVK · 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 0.98
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 5BVK · PDBe 5BVK · UniProt Q08345
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