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(-) Description

Title :  INHIBITOR BOUND STRUCTURE OF THE KINASE DOMAIN OF THE MURINE RECEPTOR TYROSINE KINASE TYRO3 (SKY)
 
Authors :  J. F. Ohren
Date :  24 Feb 11  (Deposition) - 21 Dec 11  (Release) - 11 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Kinase Inhibitor, Receptor Tyrosine Kinase, Spirocycle, Kinase Domain, Phosphotransfer, Gas6 Ligand, Cytoplasmic Surface, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. A. Powell, J. T. Kohrt, K. J. Filipski, M. Kaufman, D. Sheehan, J. E. Edmunds, A. Delaney, Y. Wang, F. Bourbonais, D. Y. Lee, F. Schwende, F. Sun, P. Mcconnell, C. Catana, H. Chen, J. Ohren, L. A. Perrin
Novel And Selective Spiroindoline-Based Inhibitors Of Sky Kinase.
Bioorg. Med. Chem. Lett. V. 22 190 2012
PubMed-ID: 22119469  |  Reference-DOI: 10.1016/J.BMCL.2011.11.036

(-) Compounds

Molecule 1 - TYROSINE-PROTEIN KINASE RECEPTOR TYRO3
    ChainsA
    EC Number2.7.10.1
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    FragmentKINASE DOMAIN
    GeneTYRO3, DTK, RSE
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    SynonymETK2/TYRO3, TK19-2, TYROSINE-PROTEIN KINASE DTK, TYROSINE- PROTEIN KINASE RSE

 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
1LUN1Ligand/Ion(5-FLUORO-1H-INDOL-2-YL)[(3R)-1'-[(3R)-PIPERIDIN-3-YL]SPIRO[INDOLE-3,3'-PYRROLIDIN]-1(2H)-YL]METHANONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:519 , LEU A:593 , PRO A:594 , PHE A:595 , MET A:596 , LYS A:597 , ARG A:649 , MET A:652 , ASP A:663BINDING SITE FOR RESIDUE LUN A 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3QUP)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3QUP)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.TYRO3_MOUSE514-540  1A:514-540
2PROTEIN_KINASE_TYRPS00109 Tyrosine protein kinases specific active-site signature.TYRO3_MOUSE641-653  1A:641-653

(-) Exons   (0, 0)

(no "Exon" information available for 3QUP)

(-) 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:241
 aligned with TYRO3_MOUSE | P55144 from UniProtKB/Swiss-Prot  Length:880

    Alignment length:284
                                   508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718       728       738       748       758       768       778    
          TYRO3_MOUSE   499 EDVLIPEQQFTLGRMLGKGEFGSVREAQLKQEDGSFVKVAVKMLKADIIASSDIEEFLREAACMKEFDHPHVAKLVGVSLRSRAKGRLPIPMVILPFMKHGDLHAFLLASRIGENPFNLPLQTLVRFMVDIACGMEYLSSRNFIHRDLAARNCMLAEDMTVCVADFGLSRKIYSGDYYRQGCASKLPVKWLALESLADNLYTVHSDVWAFGVTMWEIMTRGQTPYAGIENAEIYNYLIGGNRLKQPPECMEEVYDLMYQCWSADPKQRPSFTCLRMELENILGH 782
               SCOP domains d3qupa   _ A: automated match       es                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......---.eeeeeeeee..eeeeeee.-------..eeeee.------hhhhhhhhhhhhhhh...........eeee..-------.eeeeee.....hhhhhhhhhhh---....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.....-----------------.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh..........hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------PROTEIN_KINASE_ATP         ----------------------------------------------------------------------------------------------------PROTEIN_KINAS--------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3qup A 499 EDVLIP---FTLGRMLGKGEFGSVREAQL-------VKVAVKML------SSDIEEFLREAACMKEFDHPHVAKLVGVSLRS-------IPMVILPFMKHGDLHAFLLASRI---PFNLPLQTLVRFMVDIACGMEYLSSRNFIHRDLAARNCMLAEDMTVCVADFGL-----------------LPVKWLALESLADNLYTVHSDVWAFGVTMWEIMTRGQTPYAGIENAEIYNYLIGGNRLKQPPECMEEVYDLMYQCWSADPKQRPSFTCLRMELENILGH 782
                                 | 508       518        |-      |538   |     -|      558       568       578 |     588       598       608 |   | 618       628       638       648       658       | -         -     | 688       698       708       718       728       738       748       758       768       778    
                               504 508                527     535    542    549                            580     588                   610 614                                                 666               684                                                                                                  

   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3QUP)

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TYRO3_MOUSE | P55144)
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: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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    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: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.
    GO:0004714    transmembrane receptor protein tyrosine kinase activity    Combining with a signal and transmitting the signal from one side of the membrane to the other to initiate a change in cell activity by catalysis of the reaction: ATP + a protein-L-tyrosine = ADP + a protein-L-tyrosine phosphate.
biological process
    GO:0043277    apoptotic cell clearance    The recognition and removal of an apoptotic cell by a neighboring cell or by a phagocyte.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0021885    forebrain cell migration    The orderly movement of a cell from one site to another at least one of which is located in the forebrain.
    GO:0001779    natural killer cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a natural killer cell.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0045824    negative regulation of innate immune response    Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response.
    GO:0051250    negative regulation of lymphocyte activation    Any process that stops, prevents, or reduces the frequency, rate or extent of lymphocyte activation.
    GO:0043524    negative regulation of neuron apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process in neurons.
    GO:0034122    negative regulation of toll-like receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor signaling pathway.
    GO:0070050    neuron cellular homeostasis    The cellular homeostatic process that preserves a neuron in a stable, differentiated functional and structural state.
    GO:0042698    ovulation cycle    The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    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:0070527    platelet aggregation    The adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0043491    protein kinase B signaling    A series of reactions, mediated by the intracellular serine/threonine kinase protein kinase B (also called AKT), which occurs as a result of a single trigger reaction or compound.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0032940    secretion by cell    The controlled release of a substance by a cell.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0034446    substrate adhesion-dependent cell spreading    The morphogenetic process that results in flattening of a cell as a consequence of its adhesion to a substrate.
    GO:0060068    vagina development    The reproductive developmental process whose specific outcome is the progression of the vagina over time, from its formation to the mature structure.
cellular component
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005635    nuclear envelope    The double lipid bilayer enclosing the nucleus and separating its contents from the rest of the cytoplasm; includes the intermembrane space, a gap of width 20-40 nm (also called the perinuclear space).
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    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

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        TYRO3_MOUSE | P551444feq 4ff8

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