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Title :   STRUCTURE OF NEK2 BOUND TO AMINIPYRAZINE COMPOUND 5

Authors :   C. Mas-Droux, R. Bayliss

Date :   07 Jul 10 (Deposition) - 03 Nov 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

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE NEK2
	Chains	:	A
	EC Number	:	2.7.11.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 1-271
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	NEK2, NEVER IN MITOSIS A-RELATED KINASE 2, NIMA-RELATED PROTEIN KINASE 2, NIMA-LIKE PROTEIN KINASE 1, HSPK 21

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 5)

No.	Name	Count	Type	Full Name
1	CL	4	Ligand/Ion	CHLORIDE ION
2	WI2	1	Ligand/Ion	1-[3-AMINO-6-(3-METHOXYPHENYL)PYRAZIN-2-YL]PIPERIDINE-4-CARBOXYLIC ACID

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	CYS A:22 , LYS A:37 , TYR A:70 , MET A:86 , GLU A:87 , CYS A:89 , GLY A:92 , PHE A:148 , ASP A:159 , HOH A:2123	BINDING SITE FOR RESIDUE WI2 A1280
2	AC2	SOFTWARE	ARG A:235 , HOH A:2035	BINDING SITE FOR RESIDUE CL A1282
3	AC3	SOFTWARE	ASN A:154 , HIS A:277 , HOH A:2065	BINDING SITE FOR RESIDUE CL A1283

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

(no "Cis Peptide Bond" information available for 2XKE)

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

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	NEK2_HUMAN	137-149	1	A:141-149

Asymmetric/Biological Unit (6, 6)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000366999	1a	ENSE00001443207	chr1:211848960-211848726	235	NEK2_HUMAN	1-32	32	1	A:3-32 (gaps)	30
1.2	ENST00000366999	2	ENSE00001010392	chr1:211847855-211847638	218	NEK2_HUMAN	33-105	73	1	A:33-105	73
1.3	ENST00000366999	3	ENSE00001167194	chr1:211847065-211846825	241	NEK2_HUMAN	105-185	81	1	A:105-185 (gaps)	81
1.4a	ENST00000366999	4a	ENSE00001010393	chr1:211844626-211844544	83	NEK2_HUMAN	186-213	28	1	A:186-213 (gaps)	28
1.5a	ENST00000366999	5a	ENSE00001010397	chr1:211843749-211843623	127	NEK2_HUMAN	213-255	43	1	A:213-255	43
1.6b	ENST00000366999	6b	ENSE00001010396	chr1:211842674-211842455	220	NEK2_HUMAN	256-329	74	1	A:256-279	24
1.7a	ENST00000366999	7a	ENSE00000792201	chr1:211840573-211840448	126	NEK2_HUMAN	329-371	43	0	-	-
1.8b	ENST00000366999	8b	ENSE00001443206	chr1:211836994-211836114	881	NEK2_HUMAN	371-445	75	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:243
 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 d2xkea_ A: aut   omated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----Pkinase-2   xkeA01 A:8-271                                                                                                                                                                                                                                              -------- Pfam domains
         Sec.struct. author .hhh.eeeeeeee.---.eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhh.........eeeeeee....eeeeeee....eehhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.---------..hhh.eee.....eee...------------------.....hhhhhh----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)
                 2xke A   3 SRAEDYEVLYTIGT---GRCQKIRRKSDGKILVWKELDYGSMTEAEKQMLVSEVNLLRELKHPNIVRYYDRIIDRTNTTLYIVMEYCEGGDLASVITKGTKERQYLDEEFVLRVMTQLTLALKECHRRS---------DLKPANVFLDGKQNVKLGDF------------------TPYYMSPEQMN----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  20                                                                                                            131       141                160                179       189  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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Protein kinase-like (PK-like) (2589)

Superfamily: Protein kinase-like (PK-like) (2589)

Family: Protein kinases, catalytic subunit (1977)

Protein domain: automated matches (542)

Human (Homo sapiens) [TaxId: 9606] (452)

d2xkea_

(no "CATH Domain" information available for 2XKE)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PKinase (934)

Family: Pkinase (680)

Homo sapiens (Human) (521)

Pkinase-2xkeA01

A:8-271

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.

Asymmetric/Biological Unit
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	2xke
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	NEK2_HUMAN \| P51955
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	2.7.11.1
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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
2xk3	STRUCTURE OF NEK2 BOUND TO CCT244744
2xk4	STRUCTURE OF NEK2 BOUND TO CCT242101
2xk6	STRUCTURE OF NEK2 BOUND TO
2xk7	STRUCTURE OF NEK2 BOUND TO CCT242010
2xk8	STRUCTURE OF NEK2 BOUND TO CCT241799
2xkc	STRUCTURE OF NEK2 BOUND TO CCT241734
2xkd	STRUCTURE OF NEK2 BOUND TO CCT231393
2xkf	STRUCTURE OF NEK2 BOUND TO CCT134934

Description

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Ligands, Modified Residues, Ions (2, 5)

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Exons (6, 6)

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