› 6fer

X-ray diffraction
2.87Å resolution

Crystal Structure of human DDR2 kinase in complex with 2-[4,5-difluoro-2-oxo-1'-(1H-pyrazolo[3,4-b]pyridine-5-carbonyl)spiro[indole-3,4'-piperidine]-1-yl]-N-(2,2,2-trifluoroethyl)acetamide

Released:
DOI: 10.2210/pdb6fer/pdb
PDB entry 6fer coloured by chain, front view.
PDB entry 6fer coloured by chain, side view.
PDB entry 6fer 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-172591 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Discoidin domain-containing receptor 2 Chains: A, B, C, D, E, F, G, H, I, J, K, L
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J, K, L
Length: 309 amino acids
Theoretical weight: 35.74 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q16832 (Residues: 553-855; Coverage: 36%)
Gene names: DDR2, NTRKR3, TKT, TYRO10
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand D6Q 12 x D6Q
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 70.91Å b: 155.79Å c: 355.99Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.2 0.287
Expression system: Spodoptera frugiperda

Quick links

Citations

16 review citations

Beyond protein binding: recent advances in screening DNA-encoded libraries.
Kodadek et al. (2019)
15 more