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- PDB-3oxz: Crystal structure of ABL kinase domain bound with a DFG-out inhib... -

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Basic information

Entry
Database: PDB / ID: 3oxz
TitleCrystal structure of ABL kinase domain bound with a DFG-out inhibitor AP24534
ComponentsTyrosine-protein kinase ABL1
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / protein-inhibitor complex / protein kinase two-domain fold / phosphotransferase / ATP binding / phosphorylation / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


transitional one stage B cell differentiation / Role of ABL in ROBO-SLIT signaling / cerebellum morphogenesis / DN4 thymocyte differentiation / regulation of extracellular matrix organization / HDR through Single Strand Annealing (SSA) / B cell proliferation involved in immune response / B-1 B cell homeostasis / RHO GTPases Activate WASPs and WAVEs / neuroepithelial cell differentiation ...transitional one stage B cell differentiation / Role of ABL in ROBO-SLIT signaling / cerebellum morphogenesis / DN4 thymocyte differentiation / regulation of extracellular matrix organization / HDR through Single Strand Annealing (SSA) / B cell proliferation involved in immune response / B-1 B cell homeostasis / RHO GTPases Activate WASPs and WAVEs / neuroepithelial cell differentiation / positive regulation of Wnt signaling pathway, planar cell polarity pathway / alpha-beta T cell differentiation / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / microspike assembly / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / activated T cell proliferation / protein localization to cytoplasmic microtubule plus-end / Cyclin D associated events in G1 / DNA conformation change / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / regulation of cellular senescence / response to epinephrine / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / negative regulation of ubiquitin-protein transferase activity / podocyte apoptotic process / Bergmann glial cell differentiation / regulation of postsynaptic specialization assembly / positive regulation of phospholipase C/protein kinase C signal transduction / regulation of modification of synaptic structure / delta-catenin binding / RUNX1 regulates transcription of genes involved in differentiation of HSCs / circulatory system development / positive regulation of extracellular matrix organization / Regulation of actin dynamics for phagocytic cup formation / neuropilin signaling pathway / neuropilin binding / Myogenesis / negative regulation of mitotic cell cycle / bubble DNA binding / spleen development / positive regulation of establishment of T cell polarity / neuromuscular process controlling balance / regulation of T cell differentiation / positive regulation of blood vessel branching / proline-rich region binding / post-embryonic development / platelet-derived growth factor receptor signaling pathway / positive regulation of dendrite development / B cell proliferation / mitogen-activated protein kinase binding / regulation of Cdc42 protein signal transduction / negative regulation of cell-cell adhesion / syntaxin binding / negative regulation of cellular senescence / regulation of axon extension / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of osteoblast proliferation / neural tube closure / thymus development / platelet-derived growth factor receptor-beta signaling pathway / cell leading edge / myoblast proliferation / negative regulation of endothelial cell apoptotic process / negative regulation of BMP signaling pathway / cardiac muscle cell proliferation / negative regulation of long-term synaptic potentiation / regulation of microtubule polymerization / associative learning / positive regulation of focal adhesion assembly / cellular response to transforming growth factor beta stimulus / ephrin receptor signaling pathway / positive regulation of vasoconstriction / positive regulation of substrate adhesion-dependent cell spreading / endothelial cell migration / positive regulation of stress fiber assembly / substrate adhesion-dependent cell spreading / negative regulation of double-strand break repair via homologous recombination / positive regulation of T cell migration / ephrin receptor binding / phagocytosis / canonical NF-kappaB signal transduction / positive regulation of mitotic cell cycle / four-way junction DNA binding / positive regulation of interleukin-2 production / ruffle / signal transduction in response to DNA damage / phosphotyrosine residue binding / actin filament polymerization / peptidyl-tyrosine phosphorylation / positive regulation of endothelial cell migration / B cell receptor signaling pathway / integrin-mediated signaling pathway / SH2 domain binding / positive regulation of fibroblast proliferation / protein serine/threonine kinase activator activity / response to endoplasmic reticulum stress / positive regulation of release of sequestered calcium ion into cytosol / protein kinase C binding / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase
Similarity search - Function
F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain ...F-actin binding / F-actin binding / F-actin binding domain (FABD) / Tyrosine-protein kinase ABL, SH2 domain / : / SH3 domain / SH2 domain / Src homology 2 (SH2) domain profile. / Src homology 2 domains / SH2 domain / Src homology 3 domains / SH2 domain superfamily / SH3-like domain superfamily / Src homology 3 (SH3) domain profile. / SH3 domain / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Tyrosine-protein kinase, active site / Protein tyrosine and serine/threonine kinase / Serine-threonine/tyrosine-protein kinase, catalytic domain / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-0LI / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsZhou, T. / Huang, W.S. / Wang, Y. / Thomas, M. / Keats, J. / Xu, Q. / Rivera, V. / Shakespeare, W.C. / Clackson, T. / Dalgarno, D.C. / Zhu, X.
CitationJournal: Chem.Biol.Drug Des. / Year: 2011
Title: Structural Mechanism of the Pan-BCR-ABL Inhibitor Ponatinib (AP24534): Lessons for Overcoming Kinase Inhibitor Resistance.
Authors: Zhou, T. / Commodore, L. / Huang, W.S. / Wang, Y. / Thomas, M. / Keats, J. / Xu, Q. / Rivera, V.M. / Shakespeare, W.C. / Clackson, T. / Dalgarno, D.C. / Zhu, X.
History
DepositionSep 22, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 15, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,3302
Polymers32,7971
Non-polymers5331
Water1,60389
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.883, 59.906, 66.281
Angle α, β, γ (deg.)90.000, 96.010, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Tyrosine-protein kinase ABL1 / Abelson murine leukemia viral oncogene homolog 1 / Proto-oncogene c-Abl / p150


Mass: 32797.438 Da / Num. of mol.: 1 / Fragment: UNP residues 229-511
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abl1, Abl / Production host: Escherichia coli (E. coli)
References: UniProt: P00520, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-0LI / 3-(imidazo[1,2-b]pyridazin-3-ylethynyl)-4-methyl-N-{4-[(4-methylpiperazin-1-yl)methyl]-3-(trifluoromethyl)phenyl}benzam ide / Ponatinib


Mass: 532.559 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H27F3N6O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 89 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.52 Å3/Da / Density % sol: 51.22 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 30% w/v polyethylene glycol, 0.2 M sodium acetate, 0.1 M Tris-HCl, pH 8.5 , VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-BM / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Nov 28, 2006
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.2→50 Å / Num. all: 16703 / Num. obs: 15384 / % possible obs: 92.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1
Reflection shellResolution: 2.2→2.28 Å / % possible all: 89.2

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Processing

Software
NameVersionClassificationNB
CNS1refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
HKL-2000data reduction
HKL-3000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IEP

1iep


Resolution: 2.2→50 Å / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2613 758 4.5 %RANDOM
Rwork0.2184 ---
all-16703 --
obs-15384 92.1 %-
Displacement parametersBiso max: 66.56 Å2 / Biso mean: 34.1192 Å2 / Biso min: 17.3 Å2
Baniso -1Baniso -2Baniso -3
1-1.279 Å20 Å20.038 Å2
2---0.706 Å20 Å2
3----0.572 Å2
Refinement stepCycle: LAST / Resolution: 2.2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2152 0 39 89 2280
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_mcbond_it1.2931.5
X-RAY DIFFRACTIONc_scbond_it2.0112
X-RAY DIFFRACTIONc_mcangle_it2.0472
X-RAY DIFFRACTIONc_scangle_it2.8732.5
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1protein_rep.param
X-RAY DIFFRACTION2dna-rna_rep.param
X-RAY DIFFRACTION3water_rep.param
X-RAY DIFFRACTION4ion.param
X-RAY DIFFRACTION5534.param

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