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(-) Description

Title :  CRYSTAL STRUCTURE OF ITK INHIBITOR COMPLEX
 
Authors :  K. Brown, G. M. T. Cheetham
Date :  25 Jan 11  (Deposition) - 22 Jun 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Protein Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. D. Charrier, A. Miller, D. P. Kay, G. Brenchley, H. C. Twin, P. N. Collier, S. Ramaya, S. B. Keily, S. J. Durrant, R. M. Knegtel, A. J. Tanner, K. Brown, A. P. Curnock, J. M. Jimenez
Discovery And Structure-Activity Relationship Of 3-Aminopyrid-2-Ones As Potent And Selective Interleukin-2 Inducible T-Cell Kinase (Itk) Inhibitors
J. Med. Chem. V. 54 2341 2011
PubMed-ID: 21391610  |  Reference-DOI: 10.1021/JM101499U

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE ITK/TSK
    ChainsA, B
    EC Number2.7.10.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 357-620
    GeneITK, EMT, LYK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymKINASE EMT, T-CELL-SPECIFIC KINASE, TYROSINE-PROTEIN KINASE LYK

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1L7O1Ligand/IonN-{5-[2-(METHYLAMINO)PYRIMIDIN-4-YL]-2-OXO-1,2-DIHYDROPYRIDIN-3-YL}-4-(PIPERIDIN-1-YL)BENZAMIDE
2PQC1Ligand/Ion3-[(8-PHENYLTHIENO[2,3-H]QUINAZOLIN-2-YL)AMINO]BENZENESULFONAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1L7O-1Ligand/IonN-{5-[2-(METHYLAMINO)PYRIMIDIN-4-YL]-2-OXO-1,2-DIHYDROPYRIDIN-3-YL}-4-(PIPERIDIN-1-YL)BENZAMIDE
2PQC1Ligand/Ion3-[(8-PHENYLTHIENO[2,3-H]QUINAZOLIN-2-YL)AMINO]BENZENESULFONAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1L7O1Ligand/IonN-{5-[2-(METHYLAMINO)PYRIMIDIN-4-YL]-2-OXO-1,2-DIHYDROPYRIDIN-3-YL}-4-(PIPERIDIN-1-YL)BENZAMIDE
2PQC-1Ligand/Ion3-[(8-PHENYLTHIENO[2,3-H]QUINAZOLIN-2-YL)AMINO]BENZENESULFONAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:369 , GLY A:370 , VAL A:377 , ALA A:389 , LYS A:391 , PHE A:435 , GLU A:436 , PHE A:437 , MET A:438 , GLY A:441 , CYS A:442 , LEU A:489 , PHE B:365 , VAL B:366BINDING SITE FOR RESIDUE PQC A 1
2AC2SOFTWAREILE B:369 , ALA B:389 , LYS B:391 , GLU B:406 , VAL B:419 , PHE B:435 , GLU B:436 , PHE B:437 , MET B:438 , GLU B:439 , GLY B:441 , LEU B:489 , ASP B:500BINDING SITE FOR RESIDUE L7O B 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3QGY)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ala A:429 -Pro A:430

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041712R451QITK_HUMANUnclassified779372373A/BR451Q
2UniProtVAR_041713R581WITK_HUMANPolymorphism34482255A/BR581W
3UniProtVAR_041714V587IITK_HUMANPolymorphism56005928A/BV587I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041712R451QITK_HUMANUnclassified779372373AR451Q
2UniProtVAR_041713R581WITK_HUMANPolymorphism34482255AR581W
3UniProtVAR_041714V587IITK_HUMANPolymorphism56005928AV587I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_041712R451QITK_HUMANUnclassified779372373BR451Q
2UniProtVAR_041713R581WITK_HUMANPolymorphism34482255BR581W
3UniProtVAR_041714V587IITK_HUMANPolymorphism56005928BV587I

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.ITK_HUMAN369-391
 
  2A:369-391
B:369-391
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.ITK_HUMAN478-490
 
  2A:478-490
B:478-490
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.ITK_HUMAN369-391
 
  1A:369-391
-
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.ITK_HUMAN478-490
 
  1A:478-490
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.ITK_HUMAN369-391
 
  1-
B:369-391
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.ITK_HUMAN478-490
 
  1-
B:478-490

(-) Exons   (0, 0)

(no "Exon" information available for 3QGY)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it)
Chain A from PDB  Type:PROTEIN  Length:246
 aligned with ITK_HUMAN | Q08881 from UniProtKB/Swiss-Prot  Length:620

    Alignment length:264
                                   364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614    
            ITK_HUMAN   355 KWVIDPSELTFVQEIGSGQFGLVHLGYWLNKDKVAIKTIREGAMSEEDFIEEAEVMMKLSHPKLVQLYGVCLEQAPICLVFEFMEHGCLSDYLRTQRGLFAAETLLGMCLDVCEGMAYLEEACVIHRDLAARNCLVGENQVIKVSDFGMTRFVLDDQYTSSTGTKFPVKWASPEVFSFSRYSSKSDVWSFGVLMWEVFSEGKIPYENRSNSEVVEDISTGFRLYKPRLASTHVYQIMNHCWKERPEDRPAFSRLLRQLAEIAES 618
               SCOP domains d3qgya_ A: Tyrosine-protein kinase Itk/Tsk                                                                                                                                                                                                                               SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeee..eeeeeeee...eeeeeeee.....hhhhhhhhhhhhhhh.......eeeee......eeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee....------------------.....hhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------Q---------------------------------------------------------------------------------------------------------------------------------W-----I------------------------------- SAPs(SNPs)
                    PROSITE --------------PROTEIN_KINASE_ATP     --------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qgy A 355 HMVIDPSELTFVQEIGSGQFGLVHLGYWLNKDKVAIKTIKEGSMSEDDFIEEAEVMMKLSHPKLVQLYGVCLEQAPICLVFEFMEHGCLSDYLRTQRGLFAAETLLGMCLDVCEGMAYLEEACVIHRDLAARNCLVGENQVIKVSDFG------------------PVKWASPEVFSFSRYSSKSDVWSFGVLMWEVFSEGKIPYENRSNSEVVEDISTGFRLYKPRLASTHVYQIMNHCWKERPEDRPAFSRLLRQLAEIAES 618
                                   364       374       384       394       404       414       424       434       444       454       464       474       484       494       | -         -      |524       534       544       554       564       574       584       594       604       614    
                                                                                                                                                                             502                521                                                                                                 

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with ITK_HUMAN | Q08881 from UniProtKB/Swiss-Prot  Length:620

    Alignment length:261
                                   365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615 
            ITK_HUMAN   356 WVIDPSELTFVQEIGSGQFGLVHLGYWLNKDKVAIKTIREGAMSEEDFIEEAEVMMKLSHPKLVQLYGVCLEQAPICLVFEFMEHGCLSDYLRTQRGLFAAETLLGMCLDVCEGMAYLEEACVIHRDLAARNCLVGENQVIKVSDFGMTRFVLDDQYTSSTGTKFPVKWASPEVFSFSRYSSKSDVWSFGVLMWEVFSEGKIPYENRSNSEVVEDISTGFRLYKPRLASTHVYQIMNHCWKERPEDRPAFSRLLRQLAEIA 616
               SCOP domains d3qgyb_ B: Tyrosine-protein kinase Itk/Tsk                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Pkinase_Tyr-3qgyB01 B:363-612                                                                                                                                                                                                                             ---- Pfam domains (1)
           Pfam domains (2) -------Pkinase_Tyr-3qgyB02 B:363-612                                                                                                                                                                                                                             ---- Pfam domains (2)
         Sec.struct. author .......eeeeeeeeee..eeeeeeee...eeeeeeee.....hhhhhhhhhhhhh.........eeeee......eeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee......----------------hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------Q---------------------------------------------------------------------------------------------------------------------------------W-----I----------------------------- SAPs(SNPs)
                    PROSITE -------------PROTEIN_KINASE_ATP     --------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qgy B 356 MVIDPSELTFVQEIGSGQFGLVHLGYWLNKDKVAIKTIKEGSMSEDDFIEEAEVMMKLSHPKLVQLYGVCLEQAPICLVFEFMEHGCLSDYLRTQRGLFAAETLLGMCLDVCEGMAYLEEACVIHRDLAARNCLVGENQVIKVSDFGMT----------------PVKWASPEVFSFSRYSSKSDVWSFGVLMWEVFSEGKIPYENRSNSEVVEDISTGFRLYKPRLASTHVYQIMNHCWKERPEDRPAFSRLLRQLAEIA 616
                                   365       375       385       395       405       415       425       435       445       455       465       475       485       495        |-         -     | 525       535       545       555       565       575       585       595       605       615 
                                                                                                                                                                              504              521                                                                                               

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3QGY)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (33, 33)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ITK_HUMAN | Q08881)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004715    non-membrane spanning protein tyrosine kinase activity    Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0038095    Fc-epsilon receptor signaling pathway    A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
    GO:0001865    NK T cell differentiation    The process in which a precursor cell type acquires the specialized features of a NK T cell.
    GO:0042110    T cell activation    The change in morphology and behavior of a mature or immature T cell resulting from exposure to a mitogen, cytokine, chemokine, cellular ligand, or an antigen for which it is specific.
    GO:0050852    T cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a T cell.
    GO:0007202    activation of phospholipase C activity    The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand.
    GO:0002250    adaptive immune response    An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
    GO:0006968    cellular defense response    A defense response that is mediated by cells.
    GO:0001816    cytokine production    The appearance of a cytokine due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0002376    immune system process    Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0032609    interferon-gamma production    The appearance of interferon-gamma due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels. Interferon-gamma is also known as type II interferon.
    GO:0032633    interleukin-4 production    The appearance of interleukin-4 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0038083    peptidyl-tyrosine autophosphorylation    The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0007169    transmembrane receptor protein tyrosine kinase signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
cellular component
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0031234    extrinsic component of cytoplasmic side of plasma membrane    The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ITK_HUMAN | Q088811sm2 1snu 1snx 2e6i 2lmj 2yuq 3miy 3mj1 3mj2 3qgw 3t9t 3v5j 3v5l 3v8t 3v8w 4hct 4hcu 4hcv 4kio 4l7s 4m0y 4m0z 4m12 4m13 4m14 4m15 4mf0 4mf1 4pp9 4ppa 4ppb 4ppc 4pqn 4qd6 4rfm

(-) Related Entries Specified in the PDB File

3qgw