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- PDB-4xli: Crystal structure of Abl2/Arg kinase in complex with dasatinib -

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Basic information

Entry
Database: PDB / ID: 4xli
TitleCrystal structure of Abl2/Arg kinase in complex with dasatinib
ComponentsNon-specific protein-tyrosine kinase
Keywordstransferase/transferase inhibitor / Transferase / inhibitor / kinase / transferase-transferase inhibitor complex
Function / homology
Function and homology information


histone H2AXY142 kinase activity / Role of ABL in ROBO-SLIT signaling / RAC3 GTPase cycle / Negative regulation of FLT3 / aggressive behavior / RAC1 GTPase cycle / synapse maturation / DN4 thymocyte differentiation / neuroepithelial cell differentiation / cerebellum morphogenesis ...histone H2AXY142 kinase activity / Role of ABL in ROBO-SLIT signaling / RAC3 GTPase cycle / Negative regulation of FLT3 / aggressive behavior / RAC1 GTPase cycle / synapse maturation / DN4 thymocyte differentiation / neuroepithelial cell differentiation / cerebellum morphogenesis / positive regulation of Wnt signaling pathway, planar cell polarity pathway / circulatory system development / histone H3Y41 kinase activity / regulation of extracellular matrix organization / auditory behavior / substrate-dependent cell migration, cell extension / positive regulation of establishment of T cell polarity / dendritic spine maintenance / alpha-beta T cell differentiation / adult walking behavior / exploration behavior / dendrite morphogenesis / negative regulation of cell-cell adhesion / neuron remodeling / negative regulation of Rho protein signal transduction / Bergmann glial cell differentiation / platelet-derived growth factor receptor signaling pathway / neuromuscular process controlling balance / actin filament bundle assembly / canonical NF-kappaB signal transduction / phagocytic cup / Rho protein signal transduction / phagocytosis / positive regulation of T cell migration / negative regulation of endothelial cell apoptotic process / cellular response to retinoic acid / phosphotyrosine residue binding / positive regulation of interleukin-2 production / actin filament organization / learning / post-embryonic development / establishment of localization in cell / non-membrane spanning protein tyrosine kinase activity / neural tube closure / non-specific protein-tyrosine kinase / visual learning / peptidyl-tyrosine phosphorylation / multicellular organism growth / cell-cell adhesion / positive regulation of neuron projection development / epidermal growth factor receptor signaling pathway / positive regulation of type II interferon production / neuron differentiation / intracellular protein localization / lamellipodium / actin cytoskeleton / manganese ion binding / actin cytoskeleton organization / positive regulation of cytosolic calcium ion concentration / protein tyrosine kinase activity / cytoplasmic vesicle / phospholipase C-activating G protein-coupled receptor signaling pathway / dendritic spine / positive regulation of canonical NF-kappaB signal transduction / positive regulation of ERK1 and ERK2 cascade / postsynapse / protein phosphorylation / glutamatergic synapse / magnesium ion binding / ATP binding / cytoplasm
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 / SH2 domain superfamily / Src homology 3 domains / 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-1N1 / Tyrosine-protein kinase / Tyrosine-protein kinase ABL2
Similarity search - Component
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsHa, B.H. / Boggon, T.J.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM100411 United States
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2015
Title: Structure of the ABL2/ARG kinase in complex with dasatinib.
Authors: Ha, B.H. / Simpson, M.A. / Koleske, A.J. / Boggon, T.J.
History
DepositionJan 13, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2015Group: Database references
Revision 1.2Sep 13, 2017Group: Author supporting evidence / Derived calculations / Source and taxonomy
Category: entity_src_gen / pdbx_audit_support / pdbx_struct_oper_list
Item: _entity_src_gen.pdbx_alt_source_flag / _pdbx_audit_support.funding_organization / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 25, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.4Sep 27, 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_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Non-specific protein-tyrosine kinase
B: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,5805
Polymers61,5392
Non-polymers1,0413
Water57632
1
A: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,3233
Polymers30,7691
Non-polymers5532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Non-specific protein-tyrosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2572
Polymers30,7691
Non-polymers4881
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.688, 109.688, 121.520
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65

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Components

#1: Protein Non-specific protein-tyrosine kinase


Mass: 30769.336 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Gene: Abl2 / Plasmid: pFastBac-HTA / Production host: Trichoplusia ni (cabbage looper) / Strain (production host): Hi 5
References: UniProt: F8VQH0, UniProt: Q4JIM5*PLUS, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-1N1 / N-(2-CHLORO-6-METHYLPHENYL)-2-({6-[4-(2-HYDROXYETHYL)PIPERAZIN-1-YL]-2-METHYLPYRIMIDIN-4-YL}AMINO)-1,3-THIAZOLE-5-CARBOXAMIDE / Dasatinib


Mass: 488.006 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H26ClN7O2S / Comment: medication*YM
#3: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 32 / 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: 3.38 Å3/Da / Density % sol: 63.6 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.1 M HEPES pH 7.0, 1.3M Sodium Malonate, 2.5 % Jeffamine ED-2001
PH range: 6.5-7.5 / Temp details: Room temperature

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Data collection

DiffractionMean temperature: 83 K / Ambient temp details: Cryo
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97916 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jun 7, 2014
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97916 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.712
11K, H, -L20.288
ReflectionResolution: 2.5→47.5 Å / Num. obs: 29610 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 11.1 % / Rsym value: 0.241 / Net I/σ(I): 8.5
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 11 % / Mean I/σ(I) obs: 1.17 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
PHASERphasing
HKL-2000data reduction
Cootmodel building
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2XYN

2xyn


Resolution: 2.5→47.5 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.939 / SU B: 8.866 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.055 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.205 1478 5.1 %RANDOM
Rwork0.154 ---
obs0.157 27244 99.98 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 48.8 Å2
Baniso -1Baniso -2Baniso -3
1-14.99 Å20 Å20 Å2
2--14.99 Å20 Å2
3----29.99 Å2
Refinement stepCycle: 1 / Resolution: 2.5→47.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4259 0 67 32 4358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0194446
X-RAY DIFFRACTIONr_bond_other_d0.0020.024155
X-RAY DIFFRACTIONr_angle_refined_deg2.0151.9756031
X-RAY DIFFRACTIONr_angle_other_deg1.05739600
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2865524
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.64524.01192
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.71815756
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.8421518
X-RAY DIFFRACTIONr_chiral_restr0.1110.2645
X-RAY DIFFRACTIONr_gen_planes_refined0.010.0214892
X-RAY DIFFRACTIONr_gen_planes_other0.0080.021002
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it4.2364.3422110
X-RAY DIFFRACTIONr_mcbond_other4.2364.3422108
X-RAY DIFFRACTIONr_mcangle_it6.0416.5042628
X-RAY DIFFRACTIONr_mcangle_other6.046.5042629
X-RAY DIFFRACTIONr_scbond_it4.9324.7642336
X-RAY DIFFRACTIONr_scbond_other4.9314.7642336
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other7.0716.9763404
X-RAY DIFFRACTIONr_long_range_B_refined8.91335.0285073
X-RAY DIFFRACTIONr_long_range_B_other8.91235.0385074
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 103 -
Rwork0.262 2012 -
obs--99.86 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.5516-0.50420.03481.44670.26760.7028-0.1086-0.2065-0.08160.13090.00130.30560.2162-0.14610.10730.0776-0.0280.03480.0576-0.01920.092641.50819.3702-7.0358
21.6386-0.24850.18030.98720.34860.8193-0.08230.06320.3238-0.1582-0.05120.1058-0.17990.10430.13350.0539-0.0176-0.04140.02960.00010.117960.601748.1829-18.9481
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A279 - 291
2X-RAY DIFFRACTION1A292 - 308
3X-RAY DIFFRACTION1A309 - 348
4X-RAY DIFFRACTION1A349 - 360
5X-RAY DIFFRACTION1A361 - 546
6X-RAY DIFFRACTION2B279 - 291
7X-RAY DIFFRACTION2B292 - 308
8X-RAY DIFFRACTION2B309 - 348
9X-RAY DIFFRACTION2B349 - 360
10X-RAY DIFFRACTION2B361 - 546

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