4C4J - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE-BASED DESIGN OF ORALLY BIOAVAILABLE PYRROLOPYRIDINE INHIBITORS OF THE MITOTIC KINASE MPS1

Authors :   S. Naud, I. M. Westwood, A. Faisal, P. Sheldrake, V. Bavetsias, B. Atras A. Hayes, J. Schmitt, A. Wood, V. Choi, K. Boxall, G. Mak, M. Gurden, M. V A. De Haven Brandon, A. Henley, R. Baker, C. Mcandrew, B. Matijssen, S. A. Eccles, F. I. Raynaud, S. Linardopoulos, R. Van Montfort, J. Bla

Date :   05 Sep 13 (Deposition) - 04 Dec 13 (Release) - 15 Jan 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A

Keywords :   Transferase, Mitosis, Structure-Based Drug Design (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Naud, I. M. Westwood, A. Faisal, P. W. Sheldrake, V. Bavetsias, B. Atrash, K. J. Cheung, M. Liu, A. Hayes, J. Schmitt, A. Wood, V. Choi, K. Boxall, G. Mak, M. Gurden, M. Valenti, A. De-Haven-Brandon, A. Henley, R. Baker, C. Mcandrew, B. Matijssen, R. Burke, S. Hoelder, S. A. Eccles, F. I. Raynaud, S. Linardopoulos, R. L. M. Van Montfort, J. Blagg
Structure-Based Design Of Orally Bioavailable 1H-Pyrrolo[3, 2-C]Pyridine Inhibitors Of The Mitotic Kinase Monopolar Spindle 1 (Mps1).
J. Med. Chem. V. 56 10045 2013
PubMed-ID: 24256217 | Reference-DOI: 10.1021/JM401395S

Molecule 1 - DUAL SPECIFICITY PROTEIN KINASE TTK
	Chains	:	A
	EC Number	:	2.7.12.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Variant	:	AI
	Fragment	:	KINASE DOMAIN, RESIDUES 519-808
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	PHOSPHOTYROSINE PICKED THREONINE-PROTEIN KINASE, PYT, MONOPOLAR SPINDLE KINASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE
2	X21	1	Ligand/Ion	TERT-BUTYL 6-{[2-CHLORO-4-(1-METHYL-1H-IMIDAZOL-5-YL)PHENYL]AMINO}-2-(1-METHYL-1H-PYRAZOL-4-YL)-1H-PYRROLO[3,2-C]PYRIDINE-1-CARBOXYLATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:541 , ALA A:551 , LYS A:553 , GLU A:571 , MET A:602 , GLU A:603 , CYS A:604 , GLY A:605 , ASN A:606 , ILE A:607 , ASP A:608 , SER A:611 , LEU A:654 , ILE A:663 , MET A:671	BINDING SITE FOR RESIDUE X21 A1795

(no "SS Bond" information available for 4C4J)

(no "Cis Peptide Bond" information available for 4C4J)

Asymmetric/Biological 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)

Asymmetric/Biological 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

(no "Exon" information available for 4C4J)

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:262
 aligned with TTK_HUMAN | P33981 from UniProtKB/Swiss-Prot  Length:857

    Alignment length:279
                                   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         
            TTK_HUMAN   516 ECISVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDTTSVVKDSQVGTVNYMPPEAIKDMSSSRENGKSKSKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQ 794
               SCOP domains d4c4ja_ A: automated matches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeeeeeee...eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhhh........eeeeee...eeeeeee...eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhh........hhh.eee....eee.........ee..--------.......hhhhhh...---------....hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...........hhhhhhhhhhhh........hhhhhh.hhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------N------------------------------------ SAPs(SNPs)
                    PROSITE ---------------PROTEIN_KINASE_ATP     -----------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c4j A 516 QSMSVKGRIYSILKQIGSGGSSKVFQVLNEKKQIYAIKYVNLEEADNQTLDSYRNEIAYLNKLQQHSDKIIRLYDYEITDQYIYMVMECGNIDLNSWLKKKKSIDPWERKSYWKNMLEAVHTIHQHGIVHSDLKPANFLIVDGMLKLIDFGIANQMQPDT--------VGtVNYMPPEAIKDMS---------SKISPKSDVWSLGCILYYMTYGKTPFQQIINQISKLHAIIDPNHEIEFPDIPEKDLQDVLKCCLKRDPKQRISIPELLAHPYVQIQ 794
                                   525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685|      695   |     -   |   715       725       735       745       755       765       775       785         
                                                                                                                                                                                         675      684 |          699       709                                                                                     
                                                                                                                                                                                                    686-TPO

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: automated matches (529)

Protein domain: automated matches (529)

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

d4c4ja_

(no "CATH Domain" information available for 4C4J)

(no "Pfam Domain" information available for 4C4J)

Asymmetric/Biological 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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		TPO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		X21	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4c4j)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	4c4j
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TTK_HUMAN \| P33981
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.7.12.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TTK_HUMAN \| P33981
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

4c4e	STRUCTURE-BASED DESIGN OF ORALLY BIOAVAILABLE PYRROLOPYRIDINE INHIBITORS OF THE MITOTIC KINASE MPS1
4c4f	STRUCTURE-BASED DESIGN OF ORALLY BIOAVAILABLE PYRROLOPYRIDINE INHIBITORS OF THE MITOTIC KINASE MPS1
4c4g	STRUCTURE-BASED DESIGN OF ORALLY BIOAVAILABLE PYRROLOPYRIDINE INHIBITORS OF THE MITOTIC KINASE MPS1
4c4h	STRUCTURE-BASED DESIGN OF ORALLY BIOAVAILABLE PYRROLOPYRIDINE INHIBITORS OF THE MITOTIC KINASE MPS1
4c4i	STRUCTURE-BASED DESIGN OF ORALLY BIOAVAILABLE PYRROLOPYRIDINE INHIBITORS OF THE MITOTIC KINASE MPS1

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (1, 1)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (21, 21)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File