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- PDB-1m52: Crystal Structure of the c-Abl Kinase domain in complex with PD173955 -

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Basic information

Entry
Database: PDB / ID: 1m52
TitleCrystal Structure of the c-Abl Kinase domain in complex with PD173955
ComponentsPROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1
KeywordsTRANSFERASE / KINASE / KINASE INHIBITOR / PD173955 / ACTIVATION LOOP
Function / homology
Function and homology information


Role of ABL in ROBO-SLIT signaling / positive regulation of phospholipase C/protein kinase C signal transduction / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein localization to cytoplasmic microtubule plus-end / DNA conformation change ...Role of ABL in ROBO-SLIT signaling / positive regulation of phospholipase C/protein kinase C signal transduction / HDR through Single Strand Annealing (SSA) / RHO GTPases Activate WASPs and WAVEs / Cyclin D associated events in G1 / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / Recruitment and ATM-mediated phosphorylation of repair and signaling proteins at DNA double strand breaks / Turbulent (oscillatory, disturbed) flow shear stress activates signaling by PIEZO1 and integrins in endothelial cells / protein localization to cytoplasmic microtubule plus-end / DNA conformation change / DN4 thymocyte differentiation / response to epinephrine / phospholipase C-inhibiting G protein-coupled receptor signaling pathway / podocyte apoptotic process / RUNX1 regulates transcription of genes involved in differentiation of HSCs / delta-catenin binding / transitional one stage B cell differentiation / regulation of postsynaptic specialization assembly / regulation of modification of synaptic structure / cerebellum morphogenesis / regulation of cellular senescence / neuroepithelial cell differentiation / B cell proliferation involved in immune response / positive regulation of extracellular matrix organization / Regulation of actin dynamics for phagocytic cup formation / positive regulation of Wnt signaling pathway, planar cell polarity pathway / microspike assembly / B-1 B cell homeostasis / neuropilin signaling pathway / neuropilin binding / regulation of extracellular matrix organization / Myogenesis / bubble DNA binding / positive regulation of establishment of T cell polarity / activated T cell proliferation / positive regulation of blood vessel branching / proline-rich region binding / negative regulation of mitotic cell cycle / regulation of Cdc42 protein signal transduction / circulatory system development / mitogen-activated protein kinase binding / positive regulation of cell migration involved in sprouting angiogenesis / positive regulation of dendrite development / syntaxin binding / regulation of T cell differentiation / regulation of axon extension / alpha-beta T cell differentiation / negative regulation of cell-cell adhesion / neuromuscular process controlling balance / positive regulation of osteoblast proliferation / platelet-derived growth factor receptor-beta signaling pathway / platelet-derived growth factor receptor signaling pathway / cell leading edge / Bergmann glial cell differentiation / B cell proliferation / regulation of microtubule polymerization / negative regulation of long-term synaptic potentiation / myoblast proliferation / negative regulation of cellular senescence / positive regulation of vasoconstriction / associative learning / negative regulation of BMP signaling pathway / positive regulation of focal adhesion assembly / cardiac muscle cell proliferation / ephrin receptor signaling pathway / canonical NF-kappaB signal transduction / phagocytosis / cellular response to transforming growth factor beta stimulus / negative regulation of endothelial cell apoptotic process / positive regulation of T cell migration / endothelial cell migration / negative regulation of double-strand break repair via homologous recombination / ephrin receptor binding / spleen development / four-way junction DNA binding / positive regulation of stress fiber assembly / ruffle / signal transduction in response to DNA damage / phosphotyrosine residue binding / actin filament polymerization / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of endothelial cell migration / substrate adhesion-dependent cell spreading / positive regulation of mitotic cell cycle / positive regulation of interleukin-2 production / peptidyl-tyrosine phosphorylation / SH2 domain binding / thymus development / response to endoplasmic reticulum stress / protein kinase C binding / positive regulation of release of sequestered calcium ion into cytosol / protein serine/threonine kinase activator activity / integrin-mediated signaling pathway / B cell receptor signaling pathway / post-embryonic development / non-membrane spanning protein tyrosine kinase activity / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / neural tube closure / cell-cell adhesion
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 / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / 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-P17 / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsNagar, B. / Bornmann, W. / Pellicena, P. / Schindler, T. / Veach, D. / Miller, W.T. / Clarkson, B. / Kuriyan, J.
CitationJournal: Cancer Res. / Year: 2002
Title: Crystal Structures of the Kinase Domain of c-Abl in Complex with the Small Molecule Inhibitors PD173955 and Imatinib (STI-571)
Authors: Nagar, B. / Bornmann, W. / Pellicena, P. / Schindler, T. / Veach, D. / Miller, W.T. / Clarkson, B. / Kuriyan, J.
History
DepositionJul 8, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 18, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: 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
B: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,7646
Polymers67,4872
Non-polymers1,2774
Water2,090116
1
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1872
Polymers33,7441
Non-polymers4431
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5774
Polymers33,7441
Non-polymers8343
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)115.848, 125.708, 56.718
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL1 / p150 / c-ABL


Mass: 33743.523 Da / Num. of mol.: 2 / Fragment: Kinase Domain (residues 232-503)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00520, EC: 2.7.1.112
#2: Chemical ChemComp-P17 / 6-(2,6-DICHLORO-PHENYL)-8-METHYL-2-(3-METHYLSULFANYL-PHENYLAMINO)-8H-PYRIDO[2,3-D]PYRIMIDIN-7-ONE / PD173955


Mass: 443.349 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H16Cl2N4OS
#3: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 116 / 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: 3.4 Å3/Da / Density % sol: 0.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: PEG 20000, MES, isopropanol, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 23, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 2.6→85 Å / Num. all: 25790 / Num. obs: 25520 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 44.2 Å2 / Rsym value: 0.082 / Net I/σ(I): 11.4
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2552 / Rsym value: 0.36 / % possible all: 99.4

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FPU

1fpu


Resolution: 2.6→55.25 Å / Rfactor Rfree error: 0.005 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.254 2469 9.9 %RANDOM
Rwork0.211 ---
all-24847 --
obs-24847 94.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 32.8883 Å2 / ksol: 0.367471 e/Å3
Displacement parametersBiso mean: 39.3 Å2
Baniso -1Baniso -2Baniso -3
1-7.33 Å20 Å20 Å2
2---3.55 Å20 Å2
3----3.78 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.37 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.39 Å0.28 Å
Refinement stepCycle: LAST / Resolution: 2.6→55.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4423 0 82 116 4621
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d21.7
X-RAY DIFFRACTIONc_improper_angle_d0.75
X-RAY DIFFRACTIONc_mcbond_it2.321.5
X-RAY DIFFRACTIONc_mcangle_it3.822
X-RAY DIFFRACTIONc_scbond_it3.932
X-RAY DIFFRACTIONc_scangle_it6.392.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.016 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.317 397 10.4 %
Rwork0.262 3426 -
obs--89.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2P17.PARP17.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP

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