› 4pms

X-ray diffraction
2.8Å resolution

The structure of TrkA kinase bound to the inhibitor 4-naphthalen-1-yl-1-[(5-phenyl-1,2,4-oxadiazol-3-yl)methyl]-1H-pyrrolo[3,2-c]pyridine-2-carboxylic acid

Released:
DOI: 10.2210/pdb4pms/pdb
PDB entry 4pms coloured by chain, front view.
PDB entry 4pms coloured by chain, side view.
PDB entry 4pms coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Maximizing diversity from a kinase screen: identification of novel and selective pan-Trk inhibitors for chronic pain.
Stachel SJ, Sanders JM, Henze DA, Rudd MT, Su HP, Li Y, Nanda KK, Egbertson MS, Manley PJ, Jones KL, Brnardic EJ, Green A, Grobler JA, Hanney B, Leitl M, Lai MT, Munshi V, Murphy D, Rickert K, Riley D, Krasowska-Zoladek A, Daley C, Zuck P, Kane SA, Bilodeau MT
J Med Chem 57 5800-16 (2014)
PMID: 24914455

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: 291 amino acids
Theoretical weight: 33.23 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: P04629 (Residues: 501-787; Coverage: 38%)
Gene names: MTC, NTRK1, TRK, TRKA
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand 31X 1 x 31X
Ligand CL 1 x CL
Ligand ACT 3 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: P64
Unit cell:
a: 75.78Å b: 75.78Å c: 112.19Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.168 0.164 0.24
Expression system: Spodoptera frugiperda

Quick links

Citations

12 review citations

Nerve Growth Factor and Pain Mechanisms.
Denk et al. (2017)
11 more

2 mentions without citation

The azaindole framework in the design of kinase inhibitors.
Mérour et al. (2014)
1 more