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(-) Description

Title :  STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 35
 
Authors :  C. Mas-Droux, R. Bayliss
Date :  07 Jul 10  (Deposition) - 27 Oct 10  (Release) - 25 May 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase, Centrosome, Mitosis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. K. Whelligan, S. Solanki, D. Taylor, D. W. Thomson, K. M. Cheung, K. Boxall, C. Mas-Droux, C. Barillari, S. Burns, C. G. Grummitt, I. Collins, R. L. Van Montfort, G. W. Aherne, R. Bayliss, S. Hoelder
Aminopyrazine Inhibitors Binding To An Unusual Inactive Conformation Of The Mitotic Kinase Nek2: Sar And Structural Characterization.
J. Med. Chem. V. 53 7682 2010
PubMed-ID: 20936789  |  Reference-DOI: 10.1021/JM1008727

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE NEK2
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentCATALYTIC DOMAIN, RESIDUES 1-271
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEK2, NEVER IN MITOSIS A-RELATED KINASE 2, NIMA-RELATED PROTEIN KINASE 2, NIMA-LIKE PROTEIN KINASE 1, HSPK 21

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2XK31Ligand/Ion4-[3-AMINO-6-(3-ETHYLTHIOPHEN-2-YL)PYRAZIN-2-YL]CYCLOHEXANE-1-CARBOXYLIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:14 , CYS A:22 , VAL A:35 , LYS A:37 , TYR A:70 , MET A:86 , GLU A:87 , CYS A:89 , GLU A:90 , ASP A:93 , PHE A:148 , ASP A:159 , PHE A:160BINDING SITE FOR RESIDUE XK3 A1280
2AC2SOFTWAREARG A:235BINDING SITE FOR RESIDUE CL A1281
3AC3SOFTWAREHOH A:2067BINDING SITE FOR RESIDUE CL A1282

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2XK3)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:160 -Gly A:161

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2XK3)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.NEK2_HUMAN137-149  1A:140-149

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003669991aENSE00001443207chr1:211848960-211848726235NEK2_HUMAN1-32321A:3-32 (gaps)30
1.2ENST000003669992ENSE00001010392chr1:211847855-211847638218NEK2_HUMAN33-105731A:33-10573
1.3ENST000003669993ENSE00001167194chr1:211847065-211846825241NEK2_HUMAN105-185811A:105-185 (gaps)81
1.4aENST000003669994aENSE00001010393chr1:211844626-21184454483NEK2_HUMAN186-213281A:186-213 (gaps)28
1.5aENST000003669995aENSE00001010397chr1:211843749-211843623127NEK2_HUMAN213-255431A:213-25543
1.6bENST000003669996bENSE00001010396chr1:211842674-211842455220NEK2_HUMAN256-329741A:256-27924
1.7aENST000003669997aENSE00000792201chr1:211840573-211840448126NEK2_HUMAN329-371430--
1.8bENST000003669998bENSE00001443206chr1:211836994-211836114881NEK2_HUMAN371-445750--

(-) 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:247
 aligned with NEK2_HUMAN | P51955 from UniProtKB/Swiss-Prot  Length:445

    Alignment length:277
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       
           NEK2_HUMAN     3 SRAEDYEVLYTIGTGSYGRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRSDGGHTVLHRDLKPANVFLDGKQNVKLGDFGLARILNHDTSFAKTFVGTPYYMSPEQMNRMSYNEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLIADLVADEQ 279
               SCOP domains d2xk3a_ A: aut    omated matches                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Pkinase-2    xk3A01 A:8-271                                                                                                                                                                                                                                             -------- Pfam domains
         Sec.struct. author .hhh.eeeeeeee.----.eeeeee.....eeeeeeee.hhhhhhhhhhhhhhhhhhhhh.......eeeeeee....eeeeeee....eehhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.--------...hhh.eee.....eee....---------------..............---hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhh....hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS---------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:3-32 (gaps) Exon 1.2  PDB: A:33-105 UniProt: 33-105                                  --------------------------------------------------------------------------------Exon 1.4a UniProt: 186-213  ------------------------------------------Exon 1.6b  PDB: A:256-27 Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------Exon 1.3  PDB: A:105-185 (gaps) UniProt: 105-185                                 ---------------------------Exon 1.5a  PDB: A:213-255 UniProt: 213-255 ------------------------ Transcript 1 (2)
                 2xk3 A   3 SRAEDYEVLYTIGT----RCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRS--------RDLKPANVFLDGKQNVKLGDFG---------------VGTPYYMSPEQMNR---NEKSDIWSLGCLLYELCALMPPFTAFSQKELAGKIREGKFRRIPYRYSDELNEIITRMLNLKDYHRPSVEEILENPLILEHHHHHH 279
                                    12   |    22        32        42        52        62        72        82        92       102       112       122        |-       142       152        |-         -    |  182       | - |     202       212       222       232       242       252       262       272       
                                        16   21                                                                                                           131      140                  161             177          190 194                                                                                     

   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 2XK3)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (46, 46)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NEK2_HUMAN | P51955)
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: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:0019903    protein phosphatase binding    Interacting selectively and non-covalently with any protein phosphatase.
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine 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:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    GO:0001824    blastocyst development    The process whose specific outcome is the progression of the blastocyst over time, from its formation to the mature structure. The mammalian blastocyst is a hollow ball of cells containing two cell types, the inner cell mass and the trophectoderm.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0051299    centrosome separation    The process in which duplicated centrosome components move away from each other. The centriole pair within each centrosome becomes part of a separate microtubule organizing center that nucleates a radial array of microtubules called an aster. The two asters move to opposite sides of the nucleus to form the two poles of the mitotic spindle.
    GO:0007059    chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
    GO:0051321    meiotic cell cycle    Progression through the phases of the meiotic cell cycle, in which canonically a cell replicates to produce four offspring with half the chromosomal content of the progenitor cell via two nuclear divisions.
    GO:0000070    mitotic sister chromatid segregation    The cell cycle process in which replicated homologous chromosomes are organized and then physically separated and apportioned to two sets during the mitotic cell cycle. Each replicated chromosome, composed of two sister chromatids, aligns at the cell equator, paired with its homologous partner. One homolog of each morphologic type goes into each of the resulting chromosome sets.
    GO:0090307    mitotic spindle assembly    The aggregation, arrangement and bonding together of a set of components to form the spindle that contributes to the process of mitosis.
    GO:0043392    negative regulation of DNA binding    Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:1903126    negative regulation of centriole-centriole cohesion    Any process that stops, prevents or reduces the frequency, rate or extent of centriole-centriole cohesion.
    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:0051973    positive regulation of telomerase activity    Any process that activates or increases the frequency, rate or extent of telomerase activity, the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    GO:1904355    positive regulation of telomere capping    Any process that activates or increases the frequency, rate or extent of telomere capping.
    GO:0032212    positive regulation of telomere maintenance via telomerase    Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    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:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0051988    regulation of attachment of spindle microtubules to kinetochore    Any process that modulates the frequency, rate or extent of the attachment of spindle microtubules to the kinetochore.
    GO:0046602    regulation of mitotic centrosome separation    Any process that modulates the frequency, rate or extent of the separation of duplicated centrosome components at the beginning of mitosis.
    GO:0007088    regulation of mitotic nuclear division    Any process that modulates the frequency, rate or extent of mitosis.
    GO:0051225    spindle assembly    The aggregation, arrangement and bonding together of a set of components to form the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart.
cellular component
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000777    condensed chromosome kinetochore    A multisubunit complex that is located at the centromeric region of a condensed chromosome and provides an attachment point for the spindle microtubules.
    GO:0000794    condensed nuclear chromosome    A highly compacted molecule of DNA and associated proteins resulting in a cytologically distinct nuclear chromosome.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.
    GO:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0030496    midbody    A thin cytoplasmic bridge formed between daughter cells at the end of cytokinesis. The midbody forms where the contractile ring constricts, and may persist for some time before finally breaking to complete cytokinesis.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NEK2_HUMAN | P519552jav 2w5a 2w5b 2w5h 2wqo 2xk4 2xk6 2xk7 2xk8 2xkc 2xkd 2xke 2xkf 2xnm 2xnn 2xno 2xnp 4a4x 4afe 5m51 5m53 5m55 5m57

(-) Related Entries Specified in the PDB File

2jav HUMAN KINASE WITH PYRROLE-INDOLINONE LIGAND
2w5a HUMAN NEK2 KINASE ADP-BOUND
2w5b HUMAN NEK2 KINASE ATPGAMMAS-BOUND
2w5h HUMAN NEK2 KINASE APO
2wqo STRUCTURE OF NEK2 BOUND TO THE AMINOPYRIDINE CCT241950
2xk4 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 17
2xk6 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 36
2xk7 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 23
2xk8 STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 15
2xkc STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 14
2xkd STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 12
2xke STRUCTURE OF NEK2 BOUND TO AMINIPYRAZINE COMPOUND 5
2xkf STRUCTURE OF NEK2 BOUND TO AMINOPYRAZINE COMPOUND 2
2xnm STRUCTURE OF NEK2 BOUND TO CCT
2xnn STRUCTURE OF NEK2 BOUND TO CCT242430
2xno STRUCTURE OF NEK2 BOUND TO CCT243779
2xnp STRUCTURE OF NEK2 BOUND TO CCT244858