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- PDB-3v8t: Crystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Ca... -

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Basic information

Entry
Database: PDB / ID: 3v8t
TitleCrystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Catalytic Domain with Thienopyrazolylindole Inhibitor 477
ComponentsTyrosine-protein kinase ITK/TSK
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / kinase / TRANSFERASE-TRANSFERASE INHIBITOR complex
Function / homology
Function and homology information


NK T cell differentiation / gamma-delta T cell activation / Generation of second messenger molecules / cellular defense response / FCERI mediated Ca+2 mobilization / T cell activation / positive regulation of cytokine production / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase ...NK T cell differentiation / gamma-delta T cell activation / Generation of second messenger molecules / cellular defense response / FCERI mediated Ca+2 mobilization / T cell activation / positive regulation of cytokine production / B cell receptor signaling pathway / non-membrane spanning protein tyrosine kinase activity / non-specific protein-tyrosine kinase / cell-cell junction / T cell receptor signaling pathway / adaptive immune response / intracellular signal transduction / signal transduction / zinc ion binding / ATP binding / nucleus / 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. ...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 / 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-477 / Tyrosine-protein kinase ITK/TSK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsMcLean, L.R. / Zhang, Y.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: X-ray crystallographic structure-based design of selective thienopyrazole inhibitors for interleukin-2-inducible tyrosine kinase.
Authors: McLean, L.R. / Zhang, Y. / Zaidi, N. / Bi, X. / Wang, R. / Dharanipragada, R. / Jurcak, J.G. / Gillespy, T.A. / Zhao, Z. / Musick, K.Y. / Choi, Y.M. / Barrague, M. / Peppard, J. / Smicker, M. ...Authors: McLean, L.R. / Zhang, Y. / Zaidi, N. / Bi, X. / Wang, R. / Dharanipragada, R. / Jurcak, J.G. / Gillespy, T.A. / Zhao, Z. / Musick, K.Y. / Choi, Y.M. / Barrague, M. / Peppard, J. / Smicker, M. / Duguid, M. / Parkar, A. / Fordham, J. / Kominos, D.
History
DepositionDec 23, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Sep 13, 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: Tyrosine-protein kinase ITK/TSK
B: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3445
Polymers60,4972
Non-polymers8473
Water4,972276
1
A: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6242
Polymers30,2491
Non-polymers3751
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7203
Polymers30,2491
Non-polymers4712
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2710 Å2
ΔGint-14 kcal/mol
Surface area21210 Å2
MethodPISA
Unit cell
Length a, b, c (Å)145.702, 69.684, 68.224
Angle α, β, γ (deg.)90.00, 107.78, 90.00
Int Tables number5
Space group name H-MC121

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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: 30248.551 Da / Num. of mol.: 2 / Fragment: unp residues 357-620
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ITK, EMT, LYK / Plasmid: pFastBac1 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q08881, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-477 / 3-{2-[5-(difluoromethyl)-2H-thieno[3,2-c]pyrazol-3-yl]-1H-indol-6-yl}pentan-3-ol


Mass: 375.435 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H19F2N3OS
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 276 / 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: 2.73 Å3/Da / Density % sol: 54.87 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.2
Details: 0.8M Ammonium-sulfate, 0.1 M Na-citrate, 0.15 M Mg-acetate, 10 mM DTT, pH 6.2, VAPOR DIFFUSION, temperature 294K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 8, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 43469 / % possible obs: 98.4 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.062 / Χ2: 1.472 / Net I/σ(I): 12.4
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.073.90.4143041.484197.7
2.07-2.153.90.32242871.488197.7
2.15-2.253.90.24142951.596197.9
2.25-2.373.90.18442991.445198.1
2.37-2.523.90.13943481.453198.4
2.52-2.713.80.10143471.407198.5
2.71-2.993.80.07443461.408198.7
2.99-3.423.80.04743701.446199
3.42-4.313.80.03244161.475199.1
4.31-503.70.0344571.524198.7

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
BUSTER-TNTBUSTER 2.9.1refinement
PDB_EXTRACT3.1data extraction
HKL-2000data collection
DENZOdata reduction
PHASERphasing
BUSTER2.9.1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: pdb entry 1sm2

1sm2


Resolution: 2→29.28 Å / Occupancy max: 1 / Occupancy min: 0.5 / SU R Cruickshank DPI: 0.169 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.248 2188 5.04 %RANDOM
Rwork0.2196 ---
obs0.2211 43376 98.39 %-
Displacement parametersBiso max: 151.08 Å2 / Biso mean: 31.3413 Å2 / Biso min: 10.57 Å2
Baniso -1Baniso -2Baniso -3
1-3.9278 Å20 Å2-2.8673 Å2
2---2.913 Å20 Å2
3----1.0148 Å2
Refine analyzeLuzzati coordinate error obs: 0.274 Å
Refinement stepCycle: LAST / Resolution: 2→29.28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3705 0 57 276 4038
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1282SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes78HARMONIC2
X-RAY DIFFRACTIONt_gen_planes561HARMONIC5
X-RAY DIFFRACTIONt_it3796HARMONIC20
X-RAY DIFFRACTIONt_nbd2SEMIHARMONIC5
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion487SEMIHARMONIC5
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_contact4651SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3854HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg5225HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.27
X-RAY DIFFRACTIONt_other_torsion16.17
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2599 165 5.22 %
Rwork0.2483 2993 -
all0.249 3158 -
obs--98.39 %

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