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- PDB-1fpu: CRYSTAL STRUCTURE OF ABL KINASE DOMAIN IN COMPLEX WITH A SMALL MO... -

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Basic information

Entry
Database: PDB / ID: 1fpu
TitleCRYSTAL STRUCTURE OF ABL KINASE DOMAIN IN COMPLEX WITH A SMALL MOLECULE INHIBITOR
ComponentsPROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL
KeywordsTRANSFERASE / kinase / kinase inhibitor / STI-571 / activation loop
Function / homology
Function and homology information


Role of ABL in ROBO-SLIT signaling / 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 ...Role of ABL in ROBO-SLIT signaling / 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 / transitional one stage B cell differentiation / positive regulation of phospholipase C/protein kinase C signal transduction / regulation of postsynaptic specialization assembly / regulation of modification of synaptic structure / delta-catenin binding / cerebellum morphogenesis / regulation of cellular senescence / B cell proliferation involved in immune response / neuroepithelial cell differentiation / 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 / circulatory system development / regulation of Cdc42 protein signal transduction / mitogen-activated protein kinase binding / positive regulation of dendrite development / syntaxin binding / alpha-beta T cell differentiation / regulation of T cell differentiation / regulation of axon extension / positive regulation of cell migration involved in sprouting angiogenesis / 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 / Bergmann glial cell differentiation / cell leading edge / B cell proliferation / regulation of microtubule polymerization / myoblast proliferation / negative regulation of cellular senescence / negative regulation of long-term synaptic potentiation / positive regulation of vasoconstriction / associative learning / positive regulation of focal adhesion assembly / negative regulation of BMP signaling pathway / ephrin receptor signaling pathway / cardiac muscle cell proliferation / phagocytosis / negative regulation of endothelial cell apoptotic process / cellular response to transforming growth factor beta stimulus / positive regulation of T cell migration / endothelial cell migration / negative regulation of double-strand break repair via homologous recombination / positive regulation of interleukin-2 production / ephrin receptor binding / spleen development / four-way junction DNA binding / positive regulation of stress fiber assembly / ruffle / peptidyl-tyrosine phosphorylation / signal transduction in response to DNA damage / phosphotyrosine residue binding / actin filament polymerization / canonical NF-kappaB signal transduction / positive regulation of substrate adhesion-dependent cell spreading / substrate adhesion-dependent cell spreading / positive regulation of mitotic cell cycle / positive regulation of endothelial cell migration / SH2 domain binding / response to endoplasmic reticulum stress / thymus development / positive regulation of release of sequestered calcium ion into cytosol / protein kinase C binding / B cell receptor signaling pathway / protein serine/threonine kinase activator activity / integrin-mediated signaling pathway / post-embryonic development / regulation of actin cytoskeleton organization / non-specific protein-tyrosine kinase / neural tube closure / non-membrane spanning protein tyrosine kinase activity / 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 / 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-PRC / Tyrosine-protein kinase ABL1
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsSchindler, T. / Bornmann, W. / Pellicena, P. / Miller, W.T. / Clarkson, B. / Kuriyan, J.
CitationJournal: Science / Year: 2000
Title: Structural mechanism for STI-571 inhibition of abelson tyrosine kinase.
Authors: Schindler, T. / Bornmann, W. / Pellicena, P. / Miller, W.T. / Clarkson, B. / Kuriyan, J.
History
DepositionAug 31, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 20, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Revision 1.4Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL
B: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)68,2524
Polymers67,4872
Non-polymers7652
Water1,78399
1
A: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1262
Polymers33,7441
Non-polymers3821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,1262
Polymers33,7441
Non-polymers3821
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)110.7, 146.1, 152.8
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number22
Space group name H-MF222
DetailsThere are two kinase molecules in the asymmetric unit. The biological assembly is a monomer.

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Components

#1: Protein PROTO-ONCOGENE TYROSINE-PROTEIN KINASE ABL / P150 / C-ABL


Mass: 33743.523 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Plasmid: PFASTBAC / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P00520, EC: 2.7.1.112
#2: Chemical ChemComp-PRC / N-[4-METHYL-3-[[4-(3-PYRIDINYL)-2-PYRIMIDINYL]AMINO]PHENYL]-3-PYRIDINECARBOXAMIDE


Mass: 382.418 Da / Num. of mol.: 2 / Fragment: 2-(PHENYLAMINO)-PYRIMIDINE COMPOUND / Source method: obtained synthetically / Formula: C22H18N6O
Details: chemically synthesized as described in Zimmermann J., Buchdunger E., Mett H., Meyer T., Lydon N.B. (1997) Bioorg. Med. Chem. Lett., Vol. 7, pp. 187
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 99 / 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: 2.29 Å3/Da / Density % sol: 46.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.2
Details: PEG 4000, magnesium chloride, mes, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 8
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
120 mMTris-HCl1drop
2100 mM1dropNaCl
33 mMdithiothreitol1drop
430 mg/mlprotein1drop
525 %(w/v)PEG40001reservoir
6100 mMMES- NaOH1reservoir
70.2 M1reservoirMgCl2

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Data collection

DiffractionMean temperature: 103 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9393
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Sep 5, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.4→99 Å / Num. obs: 221636 / % possible obs: 98.7 % / Redundancy: 9.3 % / Biso Wilson estimate: 61 Å2 / Rmerge(I) obs: 0.068 / Net I/σ(I): 30.9
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.216 / Num. unique all: 2190 / % possible all: 90.6
Reflection
*PLUS
Num. obs: 24122 / Num. measured all: 221636
Reflection shell
*PLUS
% possible obs: 90.6 %

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementResolution: 2.4→99 Å / Stereochemistry target values: Engh & Huber
Details: Tight, noncrystallographic restraints were utilized throughout the refinement so that the final r.m.s. deviation between the two molecules is 0.05 and 0.04 Angstrom for the N-terminal and ...Details: Tight, noncrystallographic restraints were utilized throughout the refinement so that the final r.m.s. deviation between the two molecules is 0.05 and 0.04 Angstrom for the N-terminal and the C-terminal lobes, respectively (excluding residues 229 to 337, 252, 262, 271, 294, 306, 404, 447, 450, 466, and 491, which were built in different conformations in the two molecules). The electron density map was significantly weaker for one of the two molecules in the asymmetric unit (chain ID B), and all the analysis (cf. primary citation) relied on the better-ordered one (chain ID A).
RfactorNum. reflection% reflectionSelection details
Rfree0.264 2383 -random
Rwork0.239 ---
all-24658 --
obs-24122 97.8 %-
Refinement stepCycle: LAST / Resolution: 2.4→99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4294 0 58 99 4451
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.4
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 99 Å / Rfactor obs: 0.239
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

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