› 5kmn

X-ray diffraction
2.14Å resolution

TrkA JM-kinase with 1-(2-methyl-4-phenyl-pyrimidin-5-yl)-3-[[2-(trifluoromethyl)phenyl]methyl]urea

Released:
DOI: 10.2210/pdb5kmn/pdb
PDB entry 5kmn coloured by chain, front view.
PDB entry 5kmn coloured by chain, side view.
PDB entry 5kmn coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural characterization of nonactive site, TrkA-selective kinase inhibitors.
Su HP, Rickert K, Burlein C, Narayan K, Bukhtiyarova M, Hurzy DM, Stump CA, Zhang X, Reid J, Krasowska-Zoladek A, Tummala S, Shipman JM, Kornienko M, Lemaire PA, Krosky D, Heller A, Achab A, Chamberlin C, Saradjian P, Sauvagnat B, Yang X, Ziebell MR, Nickbarg E, Sanders JM, Bilodeau MT, Carroll SS, Lumb KJ, Soisson SM, Henze DA, Cooke AJ
Proc Natl Acad Sci U S A 114 E297-E306 (2017)
PMID: 28039433

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-138088 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
High affinity nerve growth factor receptor Chain: A
Molecule details ›
Chain: A
Length: 330 amino acids
Theoretical weight: 37.29 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P04629 (Residues: 474-796; Coverage: 42%)
Gene names: MTC, NTRK1, TRK, TRKA
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand 6UK 1 x 6UK
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 17-ID
Spacegroup: P3112
Unit cell:
a: 52.15Å b: 52.15Å c: 228.53Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.195 0.194 0.222
Expression system: Spodoptera frugiperda

Quick links

Citations

6 review citations

Development of small-molecule tropomyosin receptor kinase (TRK) inhibitors for NTRK fusion cancers.
Jiang et al. (2021)
5 more

1 mention without citation

Structural characterization of nonactive site, TrkA-selective kinase inhibitors.
Su et al. (2017)