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- PDB-3v5l: Crystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Ca... -

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Basic information

Entry
Database: PDB / ID: 3v5l
TitleCrystal Structure of Interleukin-2 Inducible T-cell Kinase Itk Catalytic Domain with Thienopyrazolylindole Inhibitor 542
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-0G1 / Tyrosine-protein kinase ITK/TSK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.86 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 1.1Nov 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

Downloads & links

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Assembly

Deposited unit
A: Tyrosine-protein kinase ITK/TSK
B: Tyrosine-protein kinase ITK/TSK
C: Tyrosine-protein kinase ITK/TSK
D: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)122,8169
Polymers120,9944
Non-polymers1,8225
Water7,638424
1
A: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6802
Polymers30,2491
Non-polymers4321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7763
Polymers30,2491
Non-polymers5282
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6802
Polymers30,2491
Non-polymers4321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6802
Polymers30,2491
Non-polymers4321
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
A: Tyrosine-protein kinase ITK/TSK
hetero molecules

D: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,3604
Polymers60,4972
Non-polymers8632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,y-1/2,-z1
Buried area2460 Å2
ΔGint-3 kcal/mol
Surface area20790 Å2
MethodPISA
6
C: Tyrosine-protein kinase ITK/TSK
hetero molecules

B: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)61,4565
Polymers60,4972
Non-polymers9593
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y+1/2,-z+11
Buried area2670 Å2
ΔGint-13 kcal/mol
Surface area20820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.974, 68.912, 140.025
Angle α, β, γ (deg.)90.000, 100.520, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 4 / 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-0G1 / 3-[3-(4-methoxyphenyl)-2-(1H-thieno[3,2-c]pyrazol-3-yl)-1H-indol-6-yl]pentan-3-ol


Mass: 431.550 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C25H25N3O2S
#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.: 424 / 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: 2.7 Å3/Da / Density % sol: 54.51 %
Crystal growTemperature: 294 K / Method: vapor diffusion / pH: 6
Details: 0.8M Ammonium-sulfate, 0.1 M Na-citrate, 0.225 M Mg-acetate, 4% acetone, 10 mM DTT, pH 6.0, VAPOR DIFFUSION, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 22, 2005
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.86→50 Å / Num. obs: 106608 / % possible obs: 98.5 % / Redundancy: 3 % / Rmerge(I) obs: 0.059 / Χ2: 0.974 / Net I/σ(I): 9
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.86-1.932.50.511101270.99194.3
1.93-230.407107290.929199.8
2-2.0930.28107600.994199.8
2.09-2.2130.196107280.986199.6
2.21-2.3430.154106891.058199.2
2.34-2.5230.11106601.02198.6
2.52-2.7830.077106430.979198.2
2.78-3.183.10.05105680.974197.8
3.18-4.013.20.033107440.897198.3
4.01-503.40.028109600.933199.1

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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: 1.86→47.58 Å / Occupancy max: 1 / Occupancy min: 1 / SU R Cruickshank DPI: 0.142 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2519 5316 4.99 %RANDOM
Rwork0.2315 ---
obs0.2324 106570 98.12 %-
Displacement parametersBiso max: 101.5 Å2 / Biso mean: 28.7338 Å2 / Biso min: 9.07 Å2
Baniso -1Baniso -2Baniso -3
1-0.2476 Å20 Å25.1239 Å2
2---2.3167 Å20 Å2
3---2.0691 Å2
Refine analyzeLuzzati coordinate error obs: 0.297 Å
Refinement stepCycle: LAST / Resolution: 1.86→47.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7532 0 129 424 8085
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d2609SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes161HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1132HARMONIC5
X-RAY DIFFRACTIONt_it7703HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion982SEMIHARMONIC5
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_contact9306SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d7843HARMONIC20.007
X-RAY DIFFRACTIONt_angle_deg10625HARMONIC20.96
X-RAY DIFFRACTIONt_omega_torsion2.15
X-RAY DIFFRACTIONt_other_torsion15.77
LS refinement shellResolution: 1.86→1.91 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3587 344 4.9 %
Rwork0.3267 6678 -
all0.3282 7022 -
obs--98.12 %

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