› 6npu

X-ray diffraction
2.33Å resolution

C-abl Kinase domain with the activator(cmpd29), N-(1-(3,4-dichlorophenyl)-4,5-dihydro-1H-pyrazol-3-yl)acetamide

Released:
DOI: 10.2210/pdb6npu/pdb
Model geometry
Fit model/data
PDB entry 6npu coloured by chain, front view.
PDB entry 6npu coloured by chain, side view.
PDB entry 6npu coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Identification and Optimization of Novel Small c-Abl Kinase Activators Using Fragment and HTS Methodologies.
Simpson GL, Bertrand SM, Borthwick JA, Campobasso N, Chabanet J, Chen S, Coggins J, Cottom J, Christensen SB, Dawson HC, Evans HL, Hobbs AN, Hong X, Mangatt B, Munoz-Muriedas J, Oliff A, Qin D, Scott-Stevens P, Ward P, Washio Y, Yang J, Young RJ
J Med Chem 62 2154-2171 (2019)
PMID: 30689376

Function and Biology Details

Reaction catalysed: 
ATP + a [protein]-L-tyrosine = ADP + a [protein]-L-tyrosine phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-132620 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Tyrosine-protein kinase ABL1 Chains: A, B
Molecule details ›
Chains: A, B
Length: 298 amino acids
Theoretical weight: 34.71 KDa
Source organism: Homo sapiens
Expression system: Spodoptera aff. frugiperda 2 RZ-2014
UniProt:
  • Canonical: P00519 (Residues: 229-512; Coverage: 25%)
Gene names: ABL, ABL1, JTK7
Sequence domains: Protein tyrosine and serine/threonine kinase
Structure domains:

Ligands and Environments

5 bound ligands:
Ligand STI 2 x STI
Ligand KWV 2 x KWV
Ligand SO4 1 x SO4
Ligand GOL 2 x GOL
Ligand 2PE 1 x 2PE
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 21-ID-F
Spacegroup: P212121
Unit cell:
a: 75.093Å b: 95.643Å c: 115.535Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.196 0.193 0.234
Expression system: Spodoptera aff. frugiperda 2 RZ-2014

Quick links

Citations

4 citation in other articles

Intermolecular Interactions in Crystal Structures of Imatinib-Containing Compounds.
Vologzhanina et al. (2020)
3 more

2 mentions without citation

Molecular insights on ABL kinase activation using tree-based machine learning models and molecular docking.
Fernandes et al. (2021)
1 more