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- PDB-4m0y: Crystal structure of ITK in complex with compound 1 [4-(carbamoyl... -

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Basic information

Entry
Database: PDB / ID: 4m0y
TitleCrystal structure of ITK in complex with compound 1 [4-(carbamoylamino)-1-(naphthalen-1-yl)-1H-pyrazole-3-carboxamide]
ComponentsTyrosine-protein kinase ITK/TSK
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


gamma-delta T cell activation / NK T cell differentiation / : / Generation of second messenger molecules / cellular defense response / T cell activation / FCERI mediated Ca+2 mobilization / positive regulation of cytokine production / B cell receptor signaling pathway / non-specific protein-tyrosine kinase ...gamma-delta T cell activation / NK T cell differentiation / : / Generation of second messenger molecules / cellular defense response / T cell activation / FCERI mediated Ca+2 mobilization / positive regulation of cytokine production / B cell receptor signaling pathway / non-specific protein-tyrosine kinase / non-membrane spanning protein tyrosine kinase activity / cell-cell junction / T cell receptor signaling pathway / adaptive immune response / intracellular signal transduction / phosphorylation / signal transduction / ATP binding / nucleus / metal ion binding / plasma membrane / cytosol
Similarity search - Function
Tyrosine-protein kinase ITK, SH3 domain / Tyrosine-protein kinase ITK/TSK, catalytic domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology domain ...Tyrosine-protein kinase ITK, SH3 domain / Tyrosine-protein kinase ITK/TSK, catalytic domain / Zinc finger, Btk motif / BTK motif / Zinc finger Btk-type profile. / Bruton's tyrosine kinase Cys-rich motif / PH domain / PH domain profile. / Pleckstrin homology domain. / Pleckstrin homology 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. / PH-like domain superfamily / 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-M0Y / Tyrosine-protein kinase ITK/TSK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsHan, S. / Caspers, N.L.
CitationJournal: Biochem.J. / Year: 2014
Title: Selectively targeting an inactive conformation of interleukin-2-inducible T-cell kinase by allosteric inhibitors.
Authors: Han, S. / Czerwinski, R.M. / Caspers, N.L. / Limburg, D.C. / Ding, W. / Wang, H. / Ohren, J.F. / Rajamohan, F. / McLellan, T.J. / Unwalla, R. / Choi, C. / Parikh, M.D. / Seth, N. / Edmonds, ...Authors: Han, S. / Czerwinski, R.M. / Caspers, N.L. / Limburg, D.C. / Ding, W. / Wang, H. / Ohren, J.F. / Rajamohan, F. / McLellan, T.J. / Unwalla, R. / Choi, C. / Parikh, M.D. / Seth, N. / Edmonds, J. / Phillips, C. / Shakya, S. / Li, X. / Spaulding, V. / Hughes, S. / Cook, A. / Robinson, C. / Mathias, J.P. / Navratilova, I. / Medley, Q.G. / Anderson, D.R. / Kurumbail, R.G. / Aulabaugh, A.
History
DepositionAug 2, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 4, 2014Group: Database references
Revision 1.2Feb 28, 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 / software / 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 / _software.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 ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2403
Polymers30,6491
Non-polymers5912
Water2,918162
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)41.075, 69.084, 49.952
Angle α, β, γ (deg.)90.00, 106.59, 90.00
Int Tables number4
Space group name H-MP1211
DetailsAS PER THE AUTHORS THE BIOLOGICAL ASSEMBLY IS UNKNOWN

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Components

#1: Protein Tyrosine-protein kinase ITK/TSK / Interleukin-2-inducible T-cell kinase / IL-2-inducible T-cell kinase / Kinase EMT / T-cell-specific ...Interleukin-2-inducible T-cell kinase / IL-2-inducible T-cell kinase / Kinase EMT / T-cell-specific kinase / Tyrosine-protein kinase Lyk


Mass: 30649.004 Da / Num. of mol.: 1 / Fragment: UNP residues 354-620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITK, EMT, LYK / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q08881, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-M0Y / 4-(carbamoylamino)-1-(naphthalen-1-yl)-1H-pyrazole-3-carboxamide


Mass: 295.296 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H13N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 162 / 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: 2.22 Å3/Da / Density % sol: 44.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 12% PEG3350, 0.1M Mg acetate, 0.1M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jan 10, 2012
RadiationMonochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→40 Å / Num. obs: 28885 / % possible obs: 98 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Biso Wilson estimate: 20.23 Å2
Reflection shellResolution: 1.7→1.79 Å / % possible all: 91.4

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Processing

Software
NameVersionClassification
autoPROCdata collection
PHASERphasing
BUSTER2.11.2refinement
autoPROCdata scaling
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.7→39.35 Å / Cor.coef. Fo:Fc: 0.9453 / Cor.coef. Fo:Fc free: 0.9321 / SU R Cruickshank DPI: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.2169 1472 5.1 %RANDOM
Rwork0.1904 ---
obs0.1918 28868 97.93 %-
Displacement parametersBiso mean: 23.78 Å2
Baniso -1Baniso -2Baniso -3
1--3.3601 Å20 Å20.7125 Å2
2--1.6943 Å20 Å2
3---1.6658 Å2
Refine analyzeLuzzati coordinate error obs: 0.23 Å
Refinement stepCycle: LAST / Resolution: 1.7→39.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2114 0 44 162 2320
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.012218HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.943003HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d770SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes53HARMONIC2
X-RAY DIFFRACTIONt_gen_planes371HARMONIC5
X-RAY DIFFRACTIONt_it2218HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.91
X-RAY DIFFRACTIONt_other_torsion16.61
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion269SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact2526SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.76 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2623 144 5.27 %
Rwork0.2228 2586 -
all0.2248 2730 -
obs--97.93 %
Refinement TLS params.Method: refined / Origin x: 5.2761 Å / Origin y: 2.6185 Å / Origin z: 10.9816 Å
111213212223313233
T-0.0068 Å20.0009 Å2-0.0115 Å2--0.0828 Å20.0019 Å2---0.0641 Å2
L0.3427 °2-0.1582 °2-0.2178 °2-0.676 °20.173 °2--1.3186 °2
S0.0017 Å °-0.0074 Å °0.016 Å °0.076 Å °0.0118 Å °-0.0331 Å °0.0498 Å °0.0433 Å °-0.0135 Å °
Refinement TLS groupSelection details: { A|356 - A|618 }

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