3VQU - JenaLib

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Title :   CRYSTAL STRUCTURE OF HUMAN MPS1 CATALYTIC DOMAIN IN COMPLEX WITH 4-[(4-AMINO-5-CYANO-6-ETHOXYPYRIDIN-2- YL)AMINO]BENZAMIDE

Authors :   K. Kusakabe, N. Ide, Y. Daigo, T. Itoh, K. Higashino, Y. Okano, G. Tadano Y. Tachibana, Y. Sato, M. Inoue, T. Wada, M. Iguchi, T. Kanazawa, Y. Ish K. Dohi, S. Tagashira, Y. Kido, S. Sakamoto, K. Yasuo, M. Maeda, T. Yama M. Higaki, T. Endoh, K. Ueda, T. Shiota, H. Murai, Y. Nakamura

Date :   30 Mar 12 (Deposition) - 27 Jun 12 (Release) - 27 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

Chains :   Asym. Unit : A
Biol. Unit 1: A  (1x)
Biol. Unit 2: A  (2x)

Keywords :   Kinase, Serine/Threonine-Protein Kinase, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Kusakabe, N. Ide, Y. Daigo, T. Itoh, K. Higashino, Y. Okano, G. Tadano, Y. Tachibana, Y. Sato, M. Inoue, T. Wada, M. Iguchi, T. Kanazawa, Y. Ishioka, K. Dohi, S. Tagashira, Y. Kido, S. Sakamoto, K. Yasuo, M. Maeda, T. Yamamoto, M. Higaki, T. Endoh, K. Ueda, T. Shiota H. Murai, Y. Nakamura
Diaminopyridine-Based Potent And Selective Mps1 Kinase Inhibitors Binding To An Unusual Flipped-Peptide Conformation
Acs Med. Chem. Lett. 2012
PubMed: search | Reference-DOI: 10.1021/ML3000879

Molecule 1 - DUAL SPECIFICITY PROTEIN KINASE TTK
	Chains	:	A
	EC Number	:	2.7.12.1
	Engineered	:	YES
	Expression System	:	CELL-FREE SYNTHESIS
	Expression System Vector Type	:	PLASMID
	Fragment	:	CATALYTIC DOMAIN, RESIDUES 516-820
	Gene	:	TTK, MPS1, MPS1L1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PHOSPHOTYROSINE PICKED THREONINE-PROTEIN KINASE, PYT

		1
Asymmetric Unit	:	A
Biological Unit 1 (1x)	:	A
Biological Unit 2 (2x)	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 9)

No.	Name	Count	Type	Full Name
1	IOD	8	Ligand/Ion	IODIDE ION
2	O22	1	Ligand/Ion	4-[(4-AMINO-5-CYANO-6-ETHOXYPYRIDIN-2-YL)AMINO]BENZAMIDE

Biological Unit 1 (2, 9)

No.	Name	Count	Type	Full Name
1	IOD	8	Ligand/Ion	IODIDE ION
2	O22	1	Ligand/Ion	4-[(4-AMINO-5-CYANO-6-ETHOXYPYRIDIN-2-YL)AMINO]BENZAMIDE

Biological Unit 2 (2, 18)

No.	Name	Count	Type	Full Name
1	IOD	16	Ligand/Ion	IODIDE ION
2	O22	2	Ligand/Ion	4-[(4-AMINO-5-CYANO-6-ETHOXYPYRIDIN-2-YL)AMINO]BENZAMIDE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:657	BINDING SITE FOR RESIDUE IOD A 901
2	AC2	SOFTWARE	ILE A:738 , ASN A:739	BINDING SITE FOR RESIDUE IOD A 902
3	AC3	SOFTWARE	PRO A:713 , ILE A:782	BINDING SITE FOR RESIDUE IOD A 903
4	AC4	SOFTWARE	ASP A:775	BINDING SITE FOR RESIDUE IOD A 905
5	AC5	SOFTWARE	ILE A:759	BINDING SITE FOR RESIDUE IOD A 906
6	AC6	SOFTWARE	GLY A:605 , HOH A:1102	BINDING SITE FOR RESIDUE IOD A 907
7	AC7	SOFTWARE	ALA A:551 , MET A:602 , GLU A:603 , CYS A:604 , ASN A:606 , ILE A:607 , ASP A:608 , LEU A:654 , ILE A:663	BINDING SITE FOR RESIDUE O22 A 909

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

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

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037142	D	758	N	TTK_HUMAN	Polymorphism	2230512	A	D	758	N

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037142	D	758	N	TTK_HUMAN	Polymorphism	2230512	A	D	758	N

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

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_037142	D	758	N	TTK_HUMAN	Polymorphism	2230512	A	D	758	N

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

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	TTK_HUMAN	531-553	1	A:531-553
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	TTK_HUMAN	643-655	1	A:643-655

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	TTK_HUMAN	531-553	1	A:531-553
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	TTK_HUMAN	643-655	1	A:643-655

Biological Unit 2 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	TTK_HUMAN	531-553	2	A:531-553
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	TTK_HUMAN	643-655	2	A:643-655

(no "Exon" information available for 3VQU)

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:258
 aligned with TTK_HUMAN | P33981 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:280
                                   525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795
            TTK_HUMAN   516 ECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQT 795
               SCOP domains d3vqua_ A: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeeeeeee...eeeeeee.....eeeeeeee..-.hhhhhhhhhhhhhhhhhhhhhh.....eeeeee...eeeeee....eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eeee..eeee.........ee.----------......hhhhhhh..-----------..hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhh.hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N------------------------------------- SAPs(SNPs)
                    PROSITE ---------------PROTEIN_KINASE_ATP     -----------------------------------------------------------------------------------------PROTEIN_KINAS-------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3vqu A 516 ECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLE-ADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPD----------GTVNYMPPEAIKDMS-----------ISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQT 795
                                   525       535       545       555  | |  565       575       585       595       605       615       625       635       645       655       665        |-       685       695   |     -     | 715       725       735       745       755       765       775       785       795
                                                                    558 |                                                                                                               674        685           699         711                                                                                    
                                                                      560

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 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: automated matches (529)

Protein domain: automated matches (529)

Human (Homo sapiens) [TaxId: 9606] (438)

d3vqua_

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

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

Asymmetric Unit(hide GO term definitions)

Chain A (TTK_HUMAN | P33981)

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: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: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:0004712	protein serine/threonine/tyrosine kinase activity	Catalysis of the reactions: ATP + a protein serine = ADP + protein serine phosphate; ATP + a protein threonine = ADP + protein threonine phosphate; and ATP + a protein tyrosine = ADP + protein tyrosine 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:0051304	chromosome separation	The cell cycle process in which paired chromosomes are detached from each other. Chromosome separation begins with the release of cohesin complexes from chromosomes; in budding yeast, this includes the cleavage of cohesin complexes along the chromosome arms, followed by the separation of the centromeric regions. Chromosome separation also includes formation of chromatid axes mediated by condensins, and ends with the disentangling of inter-sister catenation catalyzed by topoisomerase II (topo II).
	GO:0007093	mitotic cell cycle checkpoint	A cell cycle checkpoint that ensures accurate chromosome replication and segregation by preventing progression through a mitotic cell cycle until conditions are suitable for the cell to proceed to the next stage.
	GO:0007094	mitotic spindle assembly checkpoint	A cell cycle checkpoint that delays the metaphase/anaphase transition of a mitotic nuclear division until the spindle is correctly assembled and chromosomes are attached to the spindle.
	GO:0007052	mitotic spindle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
	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:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0010862	positive regulation of pathway-restricted SMAD protein phosphorylation	Any process that increases the rate, frequency or extent of pathway-restricted SMAD protein phosphorylation. Pathway-restricted SMAD proteins and common-partner SMAD proteins are involved in the transforming growth factor beta receptor signaling pathways.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0007051	spindle organization	A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005819	spindle	The array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during mitosis or meiosis and serves to move the duplicated chromosomes apart.

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	3vqu
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	2.7.12.1
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(no "Related Entries Specified in the PDB File" available for 3VQU)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 9)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (2, 2)

Exons (0, 0)

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Gene Ontology (21, 21)

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