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- PDB-3v8w: Crystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Ca... -

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Basic information

Entry
Database: PDB / ID: 3v8w
TitleCrystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Catalytic Domain with Thienopyrazolylindole Inhibitor 469
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 / 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. ...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-0G2 / Tyrosine-protein kinase ITK/TSK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.27 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)61,3965
Polymers60,4972
Non-polymers8993
Water88349
1
A: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6502
Polymers30,2491
Non-polymers4021
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7463
Polymers30,2491
Non-polymers4982
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2730 Å2
ΔGint-14 kcal/mol
Surface area21140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)146.080, 69.290, 68.580
Angle α, β, γ (deg.)90.000, 108.040, 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 / Production host: Spodoptera frugiperda (fall armyworm)
References: UniProt: Q08881, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-0G2 / 3-[2-(5-phenyl-2H-thieno[3,2-c]pyrazol-3-yl)-1H-indol-6-yl]pentan-3-ol


Mass: 401.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H23N3OS
#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.: 49 / 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: 54.9 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 5.8
Details: 0.8M Ammonium-sulfate, 0.1 M Na-citrate, 0.2 M Mg-acetate, 10 mM DTT, pH 5.8, VAPOR DIFFUSION, temperature 294K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 16, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.26→50 Å / Num. obs: 30265 / % possible obs: 99.6 % / Redundancy: 4 % / Rmerge(I) obs: 0.185 / Χ2: 2.266 / Net I/σ(I): 5.9
Reflection shell
Resolution (Å)Redundancy (%)Num. unique allΧ2Diffraction-ID% possible allRmerge(I) obs
2.26-2.343.228941.313196.5
2.34-2.433.830531.593199.9
2.43-2.55429842.1031100
2.55-2.684.130121.54911000.934
2.68-2.854.130492.94511000.793
2.85-3.074.130173.80211000.58
3.07-3.384.230362.04111000.309
3.38-3.864.230482.19211000.174
3.86-4.874.230582.12811000.106
4.87-50431142.608199.60.113

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Processing

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

1sm2


Resolution: 2.27→38.5 Å / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.285 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2677 1521 5.04 %RANDOM
Rwork0.251 ---
obs0.2518 30182 99.73 %-
Displacement parametersBiso max: 124.09 Å2 / Biso mean: 52.9913 Å2 / Biso min: 24.32 Å2
Baniso -1Baniso -2Baniso -3
1-7.9375 Å20 Å2-4.1164 Å2
2---0.9824 Å20 Å2
3----6.9552 Å2
Refine analyzeLuzzati coordinate error obs: 0.474 Å
Refinement stepCycle: LAST / Resolution: 2.27→38.5 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3680 0 63 49 3792
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d1245SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes73HARMONIC2
X-RAY DIFFRACTIONt_gen_planes561HARMONIC5
X-RAY DIFFRACTIONt_it3762HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion486SEMIHARMONIC5
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_contact4149SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d3828HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg5192HARMONIC20.93
X-RAY DIFFRACTIONt_omega_torsion1.67
X-RAY DIFFRACTIONt_other_torsion18.06
LS refinement shellResolution: 2.27→2.35 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.2792 148 5.17 %
Rwork0.2392 2715 -
all0.2412 2863 -
obs--99.73 %

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