MolNFT v1 · #88102 · protein
Crystal structure of the human DDR1 kinase domain in complex with DDR1-in-1
4CKR · Epithelial discoidin domain-containing receptor 1: “Crystal structure of the human DDR1 kinase domain in complex with DDR1-in-1”. X-ray diffraction, 1 ligand (DI1), 2 pockets (best druggability 0.72). MolNFT v1 #88102 on GenesisL1…
- PDB
- 4CKR
- Type
- protein
- Length
- 295 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
- DI1
- Pockets
- 2 · best druggability 0.72
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 | 295 | 42% helix, 17% strand | Q08345 |
Ligands and binding sites
- DI1 · 4-[(4-ethylpiperazin-1-yl)methyl]-n-{4-methyl-3-[(2-oxo-2,3-dihydro-1h-indol-5-yl)oxy]phenyl}-3-(trifluoromethyl)benzamide · ligand · chains A
- EDO · 1,2-ethanediol · additive · 5 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 | 531 | 0.72 | 0.80 | 53 | DI1 |
| 2 | 174 | 0.46 | 0.75 | 22 | empty |
Compared structures
- 4CKR · Crystal structure of the human DDR1 kinase domain in complex with DDR1-IN-1 · 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 0.96
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 4CKR · PDBe 4CKR · UniProt Q08345
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