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(-) Description

Title :  CRYSTAL STRUCTURE OF FURANOPYRIMIDINE 1 BOUND TO LCK
 
Authors :  M. W. Martin
Date :  02 Jan 07  (Deposition) - 27 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Lck, Kinase Domain, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. W. Martin, J. Newcomb, J. J. Nunes, J. E. Bemis, D. C. Mcgowan, R. D. White, J. L. Buchanan, E. F. Dimauro, C. Boucher, T. Faust, F. Hsieh, X. Huang, J. H. Lee, S. Schneider, S. M. Turci, X. Zhu
Discovery Of Novel 2, 3-Diarylfuro[2, 3-B]Pyridin-4-Amines As Potent And Selective Inhibitors Of Lck: Synthesis, Sar, And Pharmacokinetic Properties.
Bioorg. Med. Chem. Lett. V. 17 2299 2007
PubMed-ID: 17276681  |  Reference-DOI: 10.1016/J.BMCL.2007.01.048
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTO-ONCOGENE TYROSINE-PROTEIN KINASE LCK
    ChainsA
    EC Number2.7.10.2
    EngineeredYES
    Expression SystemINSECT CELL
    Expression System Vector TypeBACULOVIRUS
    FragmentLCK KINASE DOMAIN, RESIDUES 230-500
    GeneLCK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymP56-LCK, LYMPHOCYTE CELL-SPECIFIC PROTEIN- TYROSINE KINASE, LSK, T CELL- SPECIFIC PROTEIN-TYROSINE KINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
19791Ligand/Ion5,6-DIPHENYL-N-(2-PIPERAZIN-1-YLETHYL)FURO[2,3-D]PYRIMIDIN-4-AMINE

(-) Sites  (0, 0)

(no "Site" information available for 2OF4)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OF4)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:310 -Pro A:311

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 3)

Asymmetric/Biological Unit (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_071291L341PLCK_HUMANDisease (IMD22)587777335AL341P
2UniProtVAR_013465A353VLCK_HUMANUnclassified  ---AA353V
3UniProtVAR_013466P447LLCK_HUMANUnclassified  ---AP447L

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.LCK_HUMAN251-273  1A:251-273
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.LCK_HUMAN360-372  1A:360-372

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003368901aENSE00001532907chr1:32716840-32716972133LCK_HUMAN-00--
1.2hENST000003368902hENSE00002175789chr1:32739926-32740035110LCK_HUMAN1-35350--
1.3aENST000003368903aENSE00001301511chr1:32740338-3274041982LCK_HUMAN36-63280--
1.3fENST000003368903fENSE00001323374chr1:32740594-3274068491LCK_HUMAN63-93310--
1.3hENST000003368903hENSE00001321874chr1:32740922-3274102099LCK_HUMAN93-126340--
1.4cENST000003368904cENSE00001299684chr1:32741170-32741273104LCK_HUMAN126-161360--
1.5ENST000003368905ENSE00001330813chr1:32741515-32741664150LCK_HUMAN161-211510--
1.6bENST000003368906bENSE00001307776chr1:32741938-32742090153LCK_HUMAN211-262521A:231-26232
1.7aENST000003368907aENSE00001327737chr1:32742208-32742387180LCK_HUMAN262-322611A:262-32261
1.8bENST000003368908bENSE00001292351chr1:32745272-3274534877LCK_HUMAN322-347261A:322-34726
1.8eENST000003368908eENSE00001706218chr1:32745442-32745595154LCK_HUMAN348-399521A:348-39952
1.9bENST000003368909bENSE00001805246chr1:32745680-32745811132LCK_HUMAN399-443451A:399-44345
1.10dENST0000033689010dENSE00001348148chr1:32751115-32751766652LCK_HUMAN443-509671A:443-50159

(-) Sequences/Alignments

Asymmetric/Biological 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:271
 aligned with LCK_HUMAN | P06239 from UniProtKB/Swiss-Prot  Length:509

    Alignment length:271
                                   240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500 
            LCK_HUMAN   231 KPWWEDEWEVPRETLKLVERLGAGQFGEVWMGYYNGHTKVAVKSLKQGSMSPDAFLAEANLMKQLQHQRLVRLYAVVTQEPIYIITEYMENGSLVDFLKTPSGIKLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDNEYTAREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTAT 501
               SCOP domains d2of4a_ A: Lymphocyte kinase (lck)                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2of4A01 A:231-318 Phosphorylase Kinase; domain 1                                        2of4A02 A:319-500 Transferase(Phosphotransferase) domain 1                                                                                                                            - CATH domains
               Pfam domains --------------Pkinase_Tyr-2of4A01 A:245-494                                                                                                                                                                                                                             ------- Pfam domains
         Sec.struct. author ..........hhh.eeeeeeeeee..eeeeeeee...eeeeeeee.....hhhhhhhhhhhhhh........eeeee.....eeeee.....hhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh...ee....hhh.eee.....eee......ee.....ee.......hhhhhhhhhhhhheehhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------P-----------V---------------------------------------------------------------------------------------------L------------------------------------------------------ SAPs(SNPs)
                    PROSITE --------------------PROTEIN_KINASE_ATP     --------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.6b  PDB: A:231-262       -----------------------------------------------------------Exon 1.8b  PDB: A:322-347 Exon 1.8e  PDB: A:348-399 UniProt: 348-399          -------------------------------------------Exon 1.10d  PDB: A:443-501 UniProt: 443-509 [INCOMPLETE]    Transcript 1 (1)
           Transcript 1 (2) -------------------------------Exon 1.7a  PDB: A:262-322 UniProt: 262-322                   ----------------------------------------------------------------------------Exon 1.9b  PDB: A:399-443 UniProt: 399-443   ---------------------------------------------------------- Transcript 1 (2)
                 2of4 A 231 KPWWEDEWEVPRETLKLVERLGAGQFGEVWMGYYNGHTKVAVKSLKQGSMSPDAFLAEANLMKQLQHQRLVRLYAVVTQEPIYIITEYMENGSLVDFLKTPSGIKLTINKLLDMAAQIAEGMAFIEERNYIHRDLRAANILVSDTLSCKIADFGLARLIEDNEYTAREGAKFPIKWTAPEAINYGTFTIKSDVWSFGILLTEIVTHGRIPYPGMTNPEVIQNLERGYRMVRPDNCPEELYQLMRLCWKERPEDRPTFDYLRSVLEDFFTAT 501
                                   240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500 

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (55, 55)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (LCK_HUMAN | P06239)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0051117    ATPase binding    Interacting selectively and non-covalently with an ATPase, any enzyme that catalyzes the hydrolysis of ATP.
    GO:0042609    CD4 receptor binding    Interacting selectively and non-covalently with a CD4, a receptor found on the surface of T cells, monocytes and macrophages.
    GO:0042610    CD8 receptor binding    Interacting selectively and non-covalently with a CD8, a receptor found on the surface of thymocytes and cytotoxic and suppressor T-lymphocytes.
    GO:0042169    SH2 domain binding    Interacting selectively and non-covalently with a SH2 domain (Src homology 2) of a protein, a protein domain of about 100 amino-acid residues and belonging to the alpha + beta domain class.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    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:0043548    phosphatidylinositol 3-kinase binding    Interacting selectively and non-covalently with a phosphatidylinositol 3-kinase, any enzyme that catalyzes the addition of a phosphate group to an inositol lipid at the 3' position of the inositol ring.
    GO:0046934    phosphatidylinositol-4,5-bisphosphate 3-kinase activity    Catalysis of the reaction: 1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + ATP = a 1-phosphatidyl-1D-myo-inositol 3,4,5-trisphosphate + ADP + 2 H(+).
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    GO:0004722    protein serine/threonine phosphatase activity    Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
    GO:0004713    protein tyrosine kinase activity    Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
    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:0050853    B cell receptor signaling pathway    A series of molecular signals initiated by the cross-linking of an antigen receptor on a B cell.
    GO:0031295    T cell costimulation    The process of providing, via surface-bound receptor-ligand pairs, a second, antigen-independent, signal in addition to that provided by the T cell receptor to augment T cell activation.
    GO:0030217    T cell differentiation    The process in which a precursor cell type acquires characteristics of a more mature T-cell. A T cell is a type of lymphocyte whose definin characteristic is the expression of a T cell receptor complex.
    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:0006919    activation of cysteine-type endopeptidase activity involved in apoptotic process    Any process that initiates the activity of the inactive enzyme cysteine-type endopeptidase in the context of an apoptotic process.
    GO:0006882    cellular zinc ion homeostasis    Any process involved in the maintenance of an internal steady state of zinc ions at the level of a cell.
    GO:0030097    hemopoiesis    The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    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:0046854    phosphatidylinositol phosphorylation    The process of introducing one or more phosphate groups into a phosphatidylinositol, any glycerophosphoinositol having one phosphatidyl group esterified to one of the hydroxy groups of inositol.
    GO:0048015    phosphatidylinositol-mediated signaling    A series of molecular signals in which a cell uses a phosphatidylinositol-mediated signaling to convert a signal into a response. Phosphatidylinositols include phosphatidylinositol (PtdIns) and its phosphorylated derivatives.
    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:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:0050870    positive regulation of T cell activation    Any process that activates or increases the frequency, rate or extent of T cell activation.
    GO:0050862    positive regulation of T cell receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of signaling pathways initiated by the cross-linking of an antigen receptor on a T cell.
    GO:2001244    positive regulation of intrinsic apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of intrinsic apoptotic signaling pathway.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    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:0050690    regulation of defense response to virus by virus    Any viral process that modulates the frequency, rate, or extent of the antiviral response of the host cell or organism.
    GO:0051249    regulation of lymphocyte activation    Any process that modulates the frequency, rate or extent of lymphocyte activation.
    GO:0014066    regulation of phosphatidylinositol 3-kinase signaling    Any process that modulates the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
    GO:0051209    release of sequestered calcium ion into cytosol    The process in which calcium ions sequestered in the endoplasmic reticulum, Golgi apparatus or mitochondria are released into the cytosolic compartment.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    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.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    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.
    GO:0001772    immunological synapse    An area of close contact between a lymphocyte (T-, B-, or natural killer cell) and a target cell formed through the clustering of particular signaling and adhesion molecules and their associated membrane rafts on both the lymphocyte and the target cell and facilitating activation of the lymphocyte, transfer of membrane from the target cell to the lymphocyte, and in some situations killing of the target cell through release of secretory granules and/or death-pathway ligand-receptor interaction.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0000242    pericentriolar material    A network of small fibers that surrounds the centrioles in cells; contains the microtubule nucleating activity of the centrosome.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        LCK_HUMAN | P062391bhf 1bhh 1cwd 1cwe 1fbz 1h92 1ijr 1kik 1lcj 1lck 1lkk 1lkl 1q68 1q69 1qpc 1qpd 1qpe 1qpj 1x27 2iim 2of2 2ofu 2ofv 2og8 2pl0 2zm1 2zm4 2zyb 3ac1 3ac2 3ac3 3ac4 3ac5 3ac8 3acj 3ack 3ad4 3ad5 3ad6 3b2w 3brh 3bym 3byo 3bys 3byu 3kmm 3kxz 3lck 3mpm 4c3f 4d8k 5mtm 5mtn

(-) Related Entries Specified in the PDB File

2of2 THE SAME PROTEIN COMPLEXED WITH FURANOPYRIDINE 8