› 5fdp

X-ray diffraction
2.25Å resolution

Structure of DDR1 receptor tyrosine kinase in complex with D2099 inhibitor at 2.25 Angstroms resolution.

Released:
DOI: 10.2210/pdb5fdp/pdb
PDB entry 5fdp coloured by chain, front view.
PDB entry 5fdp coloured by chain, side view.
PDB entry 5fdp coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-Based Design of Tetrahydroisoquinoline-7-carboxamides as Selective Discoidin Domain Receptor 1 (DDR1) Inhibitors.
Wang Z, Bian H, Bartual SG, Du W, Luo J, Zhao H, Zhang S, Mo C, Zhou Y, Xu Y, Tu Z, Ren X, Lu X, Brekken RA, Yao L, Bullock AN, Su J, Ding K
J Med Chem 59 5911-6 (2016)
PMID: 27219676

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170636 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Epithelial discoidin domain-containing receptor 1 Chain: A
Molecule details ›
Chain: A
Length: 337 amino acids
Theoretical weight: 38.28 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q08345 (Residues: 601-913; Coverage: 35%)
Gene names: CAK, DDR1, EDDR1, NEP, NTRK4, PTK3A, RTK6, TRKE
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand 5WR 1 x 5WR
Ligand PEG 1 x PEG
Ligand EDO 5 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 45.3Å b: 63.15Å c: 107.67Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.191 0.186 0.268
Expression system: Spodoptera frugiperda

Quick links

Citations

6 review citations

Discoidin domain receptors orchestrate cancer progression: A focus on cancer therapies.
Gao et al. (2021)
5 more

5 mentions without citation

What Makes a Kinase Promiscuous for Inhibitors?
Hanson et al. (2019)
4 more