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Asym./Biol. Unit (Jmol Viewer)

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

Title :   JNK1 COMPLEXED WITH A BIS-ANILINO-PYRROLOPYRIMIDINE INHIBITOR.

Authors :   S. Chamberlain, C. Atkins, F. Deanda, M. Dumble, R. Gerding, A. Groy, S. Korenchuk, R. Kumar, H. Lei, R. Mook, G. Moorthy, A. Redman, J. Rowla L. Shewchuk, G. Vicentini, J. Mosley

Date :   22 Sep 08 (Deposition) - 30 Dec 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

Keywords :   C-Jun N-Terminal Kinase, Mitogen-Activated Protein Kinase, Atp- Binding, Kinase, Nucleotide-Binding, Phosphoprotein, Serine/Threonine-Protein Kinase, Transferase, Jnk1 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. D. Chamberlain, A. M. Redman, J. W. Wilson, F. Deanda, J. B. Shotwell R. Gerding, H. Lei, B. Yang, K. L. Stevens, A. M. Hassell, L. M. Shewchuk M. A. Leesnitzer, J. L. Smith, P. Sabbatini, C. Atkins, A. Groy, J. L. Rowand, R. Kumar, R. A. Mook, G. Moorthy, S. Patnaik
Optimization Of 4, 6-Bis-Anilino-1H-Pyrrolo[2, 3-D]Pyrimidine Igf-1R Tyrosine Kinase Inhibitors Towards Jnk Selectivity.
Bioorg. Med. Chem. Lett. V. 19 360 2009
PubMed-ID: 19071018 | Reference-DOI: 10.1016/J.BMCL.2008.11.077

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 8
	Chains	:	A
	EC Number	:	2.7.11.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX 6P1
	Expression System Strain	:	BL21 DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MAPK8, JNK1, PRKM8
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	STRESS-ACTIVATED PROTEIN KINASE JNK1, C-JUN N-TERMINAL KINASE 1, JNK-46

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	GS7	1	Ligand/Ion	2-FLUORO-6-{[2-({2-METHOXY-4-[(METHYLSULFONYL)METHYL]PHENYL}AMINO)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-YL]AMINO}BENZAMIDE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:32 , GLY A:33 , SER A:34 , GLY A:35 , VAL A:40 , ALA A:53 , GLU A:109 , MET A:111 , ASP A:112 , ALA A:113 , ASN A:114 , GLN A:117 , SER A:155 , ASN A:156 , LEU A:168 , HOH A:507 , HOH A:518 , HOH A:605	BINDING SITE FOR RESIDUE GS7 A 365

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

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

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_042258	G	171	S	MK08_HUMAN	Unclassified	---	A	G	171	S

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

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MAPK	PS01351	MAP kinase signature.	MK08_HUMAN	61-163	1	A:61-163
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	MK08_HUMAN	147-159	1	A:147-159

Asymmetric/Biological Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1c	ENST00000374189	1c	ENSE00001462753	chr10:49514733-49514864	132	MK08_HUMAN	-	0	0	-	-
1.5b	ENST00000374189	5b	ENSE00002166090	chr10:49609655-49609825	171	MK08_HUMAN	1-41	41	1	A:7-41	35
1.6	ENST00000374189	6	ENSE00000883668	chr10:49612895-49613024	130	MK08_HUMAN	41-84	44	1	A:41-84	44
1.7	ENST00000374189	7	ENSE00001772891	chr10:49617922-49617980	59	MK08_HUMAN	85-104	20	1	A:85-104	20
1.8c	ENST00000374189	8c	ENSE00001723558	chr10:49618073-49618211	139	MK08_HUMAN	104-150	47	1	A:104-150	47
1.9b	ENST00000374189	9b	ENSE00001657864	chr10:49628198-49628363	166	MK08_HUMAN	151-206	56	1	A:151-206 (gaps)	56
1.10	ENST00000374189	10	ENSE00001705464	chr10:49632131-49632202	72	MK08_HUMAN	206-230	25	1	A:206-230	25
1.12e	ENST00000374189	12e	ENSE00000702776	chr10:49633931-49634113	183	MK08_HUMAN	230-291	62	1	A:230-291	62
1.12g	ENST00000374189	12g	ENSE00001263989	chr10:49634423-49634547	125	MK08_HUMAN	291-332	42	1	A:291-332	42
1.12j	ENST00000374189	12j	ENSE00000883675	chr10:49635123-49635186	64	MK08_HUMAN	333-354	22	1	A:333-354 (gaps)	22
1.13b	ENST00000374189	13b	ENSE00000702787	chr10:49639236-49639313	78	MK08_HUMAN	354-380	27	1	A:354-364	11
1.14g	ENST00000374189	14g	ENSE00001462730	chr10:49642927-49647403	4477	MK08_HUMAN	380-427	48	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
	(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:347
 aligned with MK08_HUMAN | P45983 from UniProtKB/Swiss-Prot  Length:427

    Alignment length:358
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356        
           MK08_HUMAN     7 DNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDLWSVGCIMGEMVCHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSKMLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIPDKQLDEREHTIEEWKELIYKEVMDLE 364
               SCOP domains d3elja_ A: automated matches                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 3eljA01 A:7-112 Phosphorylase Kinase; domain 1                                                            3eljA02 A:113-332 Transferase(Phosphotransferase) domain 1                                                                                                                                                                  ------     --------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee..eeeeee..eeeeeeeeee..eeeeeeee....eeeeeeeee.hhhhhhhhhhhhhhhhhhhhh.........eee..........eeeeeee...eehhhhhh...hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee.....------..............hhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhh..hhhhhhhhhhh......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh........hhhhhhhh..hhhhhhhhhhh.......-----....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ------------------------------------------------------MAPK  PDB: A:61-163 UniProt: 61-163                                                                    --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.5b  PDB: A:7-41 [INCOMPLETE]-------------------------------------------Exon 1.7            -----------------------------------------------------------------------------------------------------Exon 1.10  PDB: A:206-230------------------------------------------------------------Exon 1.12g  PDB: A:291-332                Exon 1.12j            ---------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------Exon 1.6  PDB: A:41-84 UniProt: 41-84       -------------------Exon 1.8c  PDB: A:104-150 UniProt: 104-150     Exon 1.9b  PDB: A:151-206 (gaps) UniProt: 151-206       -----------------------Exon 1.12e  PDB: A:230-291 UniProt: 230-291                   --------------------------------------------------------------Exon 1.13b  Transcript 1 (2)
                 3elj A   7 DNNFYSVEIGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAILERNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIIGLLNVFTPQKSLEEFQDVYIVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGL------SFMMTPYVVTRYYRAPEVILGMGYKENVDLWSVGCIMGEMVCHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRTYVENRPKYAGYSFEKLFPDVLFPADSEHNKLKASQARDLLSKMLVIDASKRISVDEALQHPYINVWYDPSEAEAPPPKIP-----EREHTIEEWKELIYKEVMDLE 364
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166     |   -  |    186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336 |     346       356        
                                                                                                                                                                                               172    179                                                                                                                                                            338   344

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(

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Folds(

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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)

d3elja_

Asymmetric/Biological Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

)

Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Phosphorylase Kinase; domain 1 (1392)

Homologous Superfamily: Phosphorylase Kinase; domain 1 (1392)

Human (Homo sapiens) (1036)

3eljA01

A:7-112

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Transferase(Phosphotransferase); domain 1 (1379)

Homologous Superfamily: Transferase(Phosphotransferase) domain 1 (1379)

Human (Homo sapiens) (1049)

3eljA02

A:113-332

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MK08_HUMAN | P45983)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004705	JUN kinase activity	Catalysis of the reaction: JUN + ATP = JUN phosphate + ADP. This reaction is the phosphorylation and activation of members of the JUN family, a gene family that encodes nuclear transcription factors.
	GO:0004707	MAP kinase activity	Catalysis of the reaction: protein + ATP = protein phosphate + ADP. This reaction is the phosphorylation of proteins. Mitogen-activated protein kinase; a family of protein kinases that perform a crucial step in relaying signals from the plasma membrane to the nucleus. They are activated by a wide range of proliferation- or differentiation-inducing signals; activation is strong with agonists such as polypeptide growth factors and tumor-promoting phorbol esters, but weak (in most cell backgrounds) by stress stimuli.
	GO:0019899	enzyme binding	Interacting selectively and non-covalently with any enzyme.
	GO:0042826	histone deacetylase binding	Interacting selectively and non-covalently with the enzyme histone deacetylase.
	GO:0035033	histone deacetylase regulator activity	Modulates the activity of histone deacetylase.
	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: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:0038095	Fc-epsilon receptor signaling pathway	A series of molecular signals initiated by the binding of the Fc portion of immunoglobulin E (IgE) to an Fc-epsilon receptor on the surface of a signal-receiving cell, and ending with regulation of a downstream cellular process, e.g. transcription. The Fc portion of an immunoglobulin is its C-terminal constant region.
	GO:0007254	JNK cascade	An intracellular protein kinase cascade containing at least a JNK (a MAPK), a JNKK (a MAPKK) and a JUN3K (a MAP3K). The cascade can also contain two additional tiers: the upstream MAP4K and the downstream MAP Kinase-activated kinase (MAPKAPK). The kinases in each tier phosphorylate and activate the kinases in the downstream tier to transmit a signal within a cell.
	GO:0007258	JUN phosphorylation	The process of introducing a phosphate group into a JUN protein.
	GO:0071222	cellular response to lipopolysaccharide	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
	GO:0071260	cellular response to mechanical stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a mechanical stimulus.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0032091	negative regulation of protein binding	Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
	GO:0018105	peptidyl-serine phosphorylation	The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
	GO:0018107	peptidyl-threonine phosphorylation	The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
	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:0043065	positive regulation of apoptotic process	Any process that activates or increases the frequency, rate or extent of cell death by apoptotic process.
	GO:0031281	positive regulation of cyclase activity	Any process that activates or increases the activity of a cyclase.
	GO:0090045	positive regulation of deacetylase activity	Any process that activates or increases the frequency, rate or extent of deacetylase activity, the catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule.
	GO:0010628	positive regulation of gene expression	Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
	GO:1900740	positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway	Any process that activates or increases the frequency, rate or extent of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway.
	GO:0051247	positive regulation of protein metabolic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways involving a protein.
	GO:0006468	protein phosphorylation	The process of introducing a phosphate group on to a protein.
	GO:0042752	regulation of circadian rhythm	Any process that modulates the frequency, rate or extent of a circadian rhythm. A circadian rhythm is a biological process in an organism that recurs with a regularity of approximately 24 hours.
	GO:0031063	regulation of histone deacetylation	Any process that modulates the frequency, rate or extent of the removal of acetyl groups from histones.
	GO:0016241	regulation of macroautophagy	Any process that modulates the frequency, rate or extent of macroautophagy.
	GO:0032880	regulation of protein localization	Any process that modulates the frequency, rate or extent of any process in which a protein is transported to, or maintained in, a specific location.
	GO:0051090	regulation of sequence-specific DNA binding transcription factor activity	Any process that modulates the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
	GO:0009411	response to UV	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ultraviolet radiation (UV light) stimulus. Ultraviolet radiation is electromagnetic radiation with a wavelength in the range of 10 to 380 nanometers.
	GO:0006950	response to stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
	GO:0005654	nucleoplasm	That part of the nuclear content other than the chromosomes or the nucleolus.
	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.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

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