› 3da6

X-ray diffraction
2Å resolution

Crystal Structure of human JNK3 complexed with N-(3-methyl-4-(3-(2-(methylamino)pyrimidin-4-yl)pyridin-2-yloxy)naphthalen-1-yl)-1H-benzo[d]imidazol-2-amine

Released:
DOI: 10.2210/pdb3da6/pdb
PDB entry 3da6 coloured by chain, front view.
PDB entry 3da6 coloured by chain, side view.
PDB entry 3da6 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Pyridyl-pyrimidine benzimidazole derivatives as potent, selective, and orally bioavailable inhibitors of Tie-2 kinase.
Cee VJ, Cheng AC, Romero K, Bellon S, Mohr C, Whittington DA, Bak A, Bready J, Caenepeel S, Coxon A, Deak HL, Fretland J, Gu Y, Hodous BL, Huang X, Kim JL, Lin J, Long AM, Nguyen H, Olivieri PR, Patel VF, Wang L, Zhou Y, Hughes P, Geuns-Meyer S
Bioorg Med Chem Lett 19 424-7 (2009)
PMID: 19062275

Function and Biology Details

Reaction catalysed: 
ATP + a protein = ADP + a phosphoprotein
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-156874 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Mitogen-activated protein kinase 10 Chain: A
Molecule details ›
Chain: A
Length: 364 amino acids
Theoretical weight: 42.06 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P53779 (Residues: 39-402; Coverage: 78%)
Gene names: JNK3, JNK3A, MAPK10, PRKM10, SAPK1B
Sequence domains: Protein kinase domain
Structure domains:

Ligands and Environments

1 bound ligand:
Ligand BZ9 1 x BZ9
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E+ SUPERBRIGHT
Spacegroup: P212121
Unit cell:
a: 52.483Å b: 71.283Å c: 106.957Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.259 0.256 0.32
Expression system: Escherichia coli

Quick links

Citations

2 review citations

The therapeutic journey of benzimidazoles: a review.
Bansal et al. (2012)
1 more

4 mentions without citation

Benzimidazole and its derivatives as cancer therapeutics: The potential role from traditional to precision medicine.
Lee et al. (2023)
3 more