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- PDB-3v5j: Crystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Ca... -

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Basic information

Entry
Database: PDB / ID: 3v5j
TitleCrystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Catalytic Domain with Thienopyrazolylindole Inhibitor 090
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-0F2 / Tyrosine-protein kinase ITK/TSK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.59 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 16, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 2, 2012Provider: repository / Type: Initial release
Revision 1.1Feb 19, 2020Group: Database references / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_ref_seq_dif
Item: _chem_comp.name / _entity.pdbx_description ..._chem_comp.name / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details
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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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

Downloads & links

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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)61,5986
Polymers60,4972
Non-polymers1,1014
Water97354
1
A: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7993
Polymers30,2491
Non-polymers5512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7993
Polymers30,2491
Non-polymers5512
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2830 Å2
ΔGint-22 kcal/mol
Surface area20990 Å2
MethodPISA
4
A: Tyrosine-protein kinase ITK/TSK
B: Tyrosine-protein kinase ITK/TSK
hetero molecules

A: Tyrosine-protein kinase ITK/TSK
B: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,19712
Polymers120,9944
Non-polymers2,2038
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_456-x-1,y,-z+11
Buried area1470 Å2
ΔGint-37 kcal/mol
Surface area22480 Å2
MethodPISA
5
A: Tyrosine-protein kinase ITK/TSK
B: Tyrosine-protein kinase ITK/TSK
hetero molecules

A: Tyrosine-protein kinase ITK/TSK
B: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)123,19712
Polymers120,9944
Non-polymers2,2038
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_446-x-1/2,y-1/2,-z+11
Buried area1730 Å2
ΔGint-26 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.132, 69.513, 68.244
Angle α, β, γ (deg.)90.000, 107.330, 90.000
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 / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q08881, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-0F2 / 3-[4-(2-morpholin-4-ylethoxy)-2-(1~{H}-thieno[3,2-c]pyrazol-3-yl)-1~{H}-indol-6-yl]pentan-3-ol


Mass: 454.585 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H30N4O3S
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 54 / 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: 55.02 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6.5
Details: 18% PEG3350, 0.1 M Bis-Tris, 0.12 M Li-sulfate, 4% propanol, 10 mM DTT, pH 6.5, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Sep 12, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→50 Å / Num. obs: 22802 / % possible obs: 99 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.115 / Χ2: 1.064 / Net I/σ(I): 7.9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2.5-2.593.70.79722310.989198.2
2.59-2.693.70.60822331.035198.1
2.69-2.823.70.48422541.057198.5
2.82-2.963.80.36922641.084198.6
2.96-3.153.80.25222761.108198.9
3.15-3.393.80.16622671.088199.1
3.39-3.733.80.11222821.066199.4
3.73-4.273.80.08223151.042199.6
4.27-5.383.80.06923161.09199.9
5.38-503.70.04923641.083199.9

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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: 2.59→38.65 Å / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.55 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2699 1039 5.12 %RANDOM
Rwork0.2451 ---
obs0.2463 20291 99.01 %-
Displacement parametersBiso max: 212.05 Å2 / Biso mean: 48.706 Å2 / Biso min: 12.28 Å2
Baniso -1Baniso -2Baniso -3
1-10.3198 Å20 Å2-5.8488 Å2
2---6.3626 Å20 Å2
3----3.9571 Å2
Refine analyzeLuzzati coordinate error obs: 0.444 Å
Refinement stepCycle: LAST / Resolution: 2.59→38.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3679 0 74 54 3807
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1244SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes77HARMONIC2
X-RAY DIFFRACTIONt_gen_planes555HARMONIC5
X-RAY DIFFRACTIONt_it3766HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion483SEMIHARMONIC5
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_contact4241SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3838HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg5203HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion1.75
X-RAY DIFFRACTIONt_other_torsion18.15
LS refinement shellResolution: 2.59→2.73 Å / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.3363 152 5.28 %
Rwork0.2836 2726 -
all0.2863 2878 -
obs--99.01 %

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