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- PDB-3qgy: Crystal structure of ITK inhibitor complex -

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Basic information

Entry
Database: PDB / ID: 3qgy
TitleCrystal structure of ITK inhibitor complex
ComponentsTyrosine-protein kinase ITK/TSK
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / PROTEIN 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-L7O / Chem-PQC / Tyrosine-protein kinase ITK/TSK
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsBrown, K. / Cheetham, G.M.T.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Discovery and structure-activity relationship of 3-aminopyrid-2-ones as potent and selective interleukin-2 inducible T-cell kinase (Itk) inhibitors
Authors: Charrier, J.D. / Miller, A. / Kay, D.P. / Brenchley, G. / Twin, H.C. / Collier, P.N. / Ramaya, S. / Keily, S.B. / Durrant, S.J. / Knegtel, R.M. / Tanner, A.J. / Brown, K. / Curnock, A.P. / Jimenez, J.M.
History
DepositionJan 25, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 22, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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)65,8254
Polymers64,9882
Non-polymers8372
Water9,170509
1
A: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,9272
Polymers32,4941
Non-polymers4331
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Tyrosine-protein kinase ITK/TSK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,8992
Polymers32,4941
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)125.8601, 74.3809, 78.8330
Angle α, β, γ (deg.)90.0000, 93.9867, 90.0000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Tyrosine-protein kinase ITK/TSK / Kinase EMT / T-cell-specific kinase / Tyrosine-protein kinase Lyk


Mass: 32494.090 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: Escherichia coli (E. coli)
References: UniProt: Q08881, non-specific protein-tyrosine kinase
#2: Chemical ChemComp-PQC / 3-[(8-phenylthieno[2,3-h]quinazolin-2-yl)amino]benzenesulfonamide


Mass: 432.518 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H16N4O2S2
#3: Chemical ChemComp-L7O / N-{5-[2-(methylamino)pyrimidin-4-yl]-2-oxo-1,2-dihydropyridin-3-yl}-4-(piperidin-1-yl)benzamide / 3-(4-(Piperidin-1-yl)benzoylamino)-5-(2-(methylamino)pyrimidin-4-yl)-(1H)-pyridin-2-one


Mass: 404.465 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24N6O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 509 / 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: 2.83 Å3/Da / Density % sol: 56.57 %

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.542 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2.1→20 Å / Num. all: 40537 / Num. obs: 40537 / % possible obs: 95.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0
Reflection shellResolution: 2.1→2.2 Å / % possible all: 95.5

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Processing

Software
NameClassification
CrystalCleardata collection
AMoREphasing
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→20 Å / σ(F): 4 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.247 636 RANDOM
Rwork0.208 --
obs0.208 31613 -
all-40536 -
Refinement stepCycle: LAST / Resolution: 2.1→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3924 0 60 509 4493

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