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- PDB-2hzn: Abl kinase domain in complex with NVP-AFG210 -

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Basic information

Entry
Database: PDB / ID: 2hzn
TitleAbl kinase domain in complex with NVP-AFG210
ComponentsProto-oncogene tyrosine-protein kinase ABL1
KeywordsTRANSFERASE / tyrosine kinase
Function / homology
Function and homology information


: / signal transduction in response to DNA damage => GO:0042770 / circulatory system development => GO:0072359 / : / : / : / Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / actin filament branching ...: / signal transduction in response to DNA damage => GO:0042770 / circulatory system development => GO:0072359 / : / : / : / Role of ABL in ROBO-SLIT signaling / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / actin filament branching / Cyclin D associated events in G1 / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / : / : / positive regulation of actin filament binding / positive regulation of oxidoreductase activity / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / circulatory system development / podocyte apoptotic process / DN4 thymocyte differentiation / response to epinephrine / regulation of cellular senescence / transitional one stage B cell differentiation / RUNX1 regulates transcription of genes involved in differentiation of HSCs / activation of protein kinase C activity / regulation of modification of synaptic structure / positive regulation of microtubule binding / Regulation of actin dynamics for phagocytic cup formation / delta-catenin binding / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / neuroepithelial cell differentiation / microspike assembly / positive regulation of Wnt signaling pathway, planar cell polarity pathway / collateral sprouting / regulation of extracellular matrix organization / cerebellum morphogenesis / positive regulation of blood vessel branching / B-1 B cell homeostasis / neuropilin signaling pathway / negative regulation of ubiquitin-protein transferase activity / neuropilin binding / Myogenesis / bubble DNA binding / negative regulation of protein serine/threonine kinase activity / activated T cell proliferation / regulation of Cdc42 protein signal transduction / proline-rich region binding / positive regulation of dendrite development / mitogen-activated protein kinase binding / myoblast proliferation / syntaxin binding / alpha-beta T cell differentiation / cardiac muscle cell proliferation / regulation of T cell differentiation / regulation of axon extension / positive regulation of cell migration involved in sprouting angiogenesis / negative regulation of cell-cell adhesion / B cell proliferation / cell leading edge / positive regulation of osteoblast proliferation / regulation of microtubule polymerization / platelet-derived growth factor receptor-beta signaling pathway / negative regulation of cellular senescence / positive regulation of focal adhesion assembly / associative learning / Bergmann glial cell differentiation / platelet-derived growth factor receptor signaling pathway / neuromuscular process controlling balance / negative regulation of mitotic cell cycle / negative regulation of BMP signaling pathway / negative regulation of long-term synaptic potentiation / endothelial cell migration / positive regulation of T cell migration / signal transduction in response to DNA damage / BMP signaling pathway / negative regulation of double-strand break repair via homologous recombination / negative regulation of endothelial cell apoptotic process / phagocytosis / canonical NF-kappaB signal transduction / four-way junction DNA binding / peptidyl-tyrosine autophosphorylation / positive regulation of substrate adhesion-dependent cell spreading / negative regulation of canonical NF-kappaB signal transduction / positive regulation of vasoconstriction / spleen development / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / ruffle / positive regulation of establishment of T cell polarity / ERK1 and ERK2 cascade / positive regulation of interleukin-2 production / ephrin receptor binding / actin filament polymerization / phosphotyrosine residue binding / positive regulation of endothelial cell migration / response to endoplasmic reticulum stress / positive regulation of mitotic cell cycle / substrate adhesion-dependent cell spreading
Similarity search - Function
Tyrosine-protein kinase ABL1/transforming protein Abl / 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 ...Tyrosine-protein kinase ABL1/transforming protein Abl / 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 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-KIN / Tyrosine-protein kinase ABL1 / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCowan-Jacob, S.W. / Fendrich, G. / Liebetanz, J. / Fabbro, D. / Manley, P.
CitationJournal: ACTA CRYSTALLOGR.,SECT.D / Year: 2007
Title: Structural biology contributions to the discovery of drugs to treat chronic myelogenous leukaemia.
Authors: Cowan-Jacob, S.W. / Fendrich, G. / Floersheimer, A. / Furet, P. / Liebetanz, J. / Rummel, G. / Rheinberger, P. / Centeleghe, M. / Fabbro, D. / Manley, P.W.
History
DepositionAug 9, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 16, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 27, 2011Group: Refinement description / Version format compliance
Revision 1.4Oct 18, 2017Group: Refinement description / Category: software
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Proto-oncogene tyrosine-protein kinase ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1172
Polymers33,7441
Non-polymers3731
Water00
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)105.431, 105.431, 110.358
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number98
Space group name H-MI4122

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Components

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


Mass: 33743.523 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abl1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q61258, UniProt: P00520*PLUS, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-KIN / 1-[4-(PYRIDIN-4-YLOXY)PHENYL]-3-[3-(TRIFLUOROMETHYL)PHENYL]UREA


Mass: 373.329 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14F3N3O2

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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: 2.27 Å3/Da / Density % sol: 45.84 %
Crystal growTemperature: 277 K / Method: microbatch under oil
Details: 16 % PEG 8000, 0.1 M NaCacodylate pH 6.2, 0.2 M MgAcetate, MICROBATCH UNDER OIL, temperature 277K

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Data collection

DiffractionMean temperature: 94 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.8602 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Apr 18, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8602 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 8868 / % possible obs: 99.9 % / Biso Wilson estimate: 94 Å2 / Rmerge(I) obs: 0.038 / Χ2: 0.813 / Net I/σ(I): 13.6
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.7-2.80.4578730.6321100
2.8-2.910.3278590.6581100
2.91-3.040.218620.6771100
3.04-3.20.1328870.7011100
3.2-3.40.0838690.7271100
3.4-3.660.0548850.7661100
3.66-4.030.048810.8251100
4.03-4.620.0328930.9481100
4.62-5.810.0289021.023199.9
5.81-500.0289571.182198.9

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Phasing

Phasing MRRfactor: 0.449 / Cor.coef. Fo:Fc: 0.532
Highest resolutionLowest resolution
Rotation3.5 Å34.73 Å
Translation3.5 Å34.73 Å

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Processing

Software
NameClassificationNB
BUSTER-TNTrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB Entry: 2HYY

2hyy


Resolution: 2.7→32 Å / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
Details: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that is not the terminal residue of the sequence. In all these instances the OXT was ...Details: Due to a feature in the refinement program, the structure was refined with OXT on one or more residues that is not the terminal residue of the sequence. In all these instances the OXT was changed to N of the next residue. DUE TO THE HIGH OVERALL TEMPERATURE FACTOR IN THESE CRYSTALS THE DENSITY MAPS LOOKED MUCH LOWER RESOLUTION THAN 2.7 A. AS A RESULT, NO WATER MOLECULES WERE ADDED. THE ELECTRON DENSITY FOR THE INHIBITOR IS WEAK, BUT DEFINITELY PRESENT. THE HIGH OVERALL B-VALUE IS PROBABLY CORRELATED WITH THE DIFFICULTY IN GETTING A MODEL WHICH GIVES A LOW R-FACTOR FOR THIS CRYSTAL FORM.
RfactorNum. reflection% reflectionSelection details
Rfree0.314 422 4.8 %RANDOM
Rwork0.264 ---
obs0.267 8864 --
Displacement parametersBiso mean: 80.24 Å2
Refinement stepCycle: LAST / Resolution: 2.7→32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2182 0 27 0 2209
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONt_bond_d0.01
X-RAY DIFFRACTIONt_angle_deg1.16

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