› 6fex

X-ray diffraction
1.29Å resolution

DDR1, 2-[4-bromo-2-oxo-1'-(1H-pyrazolo[4,3-b]pyridine-5-carbonyl)spiro[indole-3,4'-piperidine]-1-yl]-N-(2,2,2-trifluoroethyl)acetamide, 1.291A, P212121, Rfree=17.4%

Released:
DOI: 10.2210/pdb6fex/pdb
PDB entry 6fex coloured by chain, front view.
PDB entry 6fex coloured by chain, side view.
PDB entry 6fex coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
DNA-Encoded Library-Derived DDR1 Inhibitor Prevents Fibrosis and Renal Function Loss in a Genetic Mouse Model of Alport Syndrome.
Richter H, Satz AL, Bedoucha M, Buettelmann B, Petersen AC, Harmeier A, Hermosilla R, Hochstrasser R, Burger D, Gsell B, Gasser R, Huber S, Hug MN, Kocer B, Kuhn B, Ritter M, Rudolph MG, Weibel F, Molina-David J, Kim JJ, Santos JV, Stihle M, Georges GJ, Bonfil RD, Fridman R, Uhles S, Moll S, Faul C, Fornoni A, Prunotto M
ACS Chem Biol 14 37-49 (2019)
PMID: 30452219

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: 321 amino acids
Theoretical weight: 36.5 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q08345 (Residues: 593-913; 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

4 bound ligands:
Ligand D6Z 1 x D6Z
Ligand IOD 4 x IOD
Ligand MES 1 x MES
Ligand CL 4 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 40.834Å b: 61.75Å c: 63.072Å
α: 90° β: 106.51° γ: 90°
R-values:
R R work R free
0.139 0.137 0.174
Expression system: Spodoptera frugiperda

Quick links

Citations

15 review citations

Complexities of the glomerular basement membrane.
Naylor et al. (2021)
14 more

2 mentions without citation

Small-molecule discovery through DNA-encoded libraries.
Peterson et al. (2023)
1 more