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Asym./Biol. Unit (Jmol Viewer)

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

Title :   DESIGN AND SYNTHESIS OF A NOVEL, ORALLY EFFICACIOUS TRI-SUBSTITUTED THIOPHENE BASED JNK INHIBITOR

Authors :   S. Bowers, A. P. Truong, J. Neitz, M. Neitzel, G. D. Probst, R. K. Hom, A. W H. L. Sham, G. Toth, H. Pan, N. Yao, D. R. Artis, E. F. Brigham, K. P. Quinn K. Powell, L. Ruslim, F. Bard, T. A. Yednock, I. Griswold-Prenner

Date :   02 Dec 10 (Deposition) - 02 Mar 11 (Release) - 23 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.43

Chains :   Asym./Biol. Unit : A,J

Keywords :   Jnk Inhibitor, Thiophene, Neurodegeneration, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Bowers, A. P. Truong, R. J. Neitz, M. Neitzel, G. D. Probst, R. K. Hom, B. Peterson, R. A. Galemmo, A. W. Konradi, H. L. Sham, G. Toth, H. Pan, N. Yao, D. R. Artis, E. F. Brigham, K. P. Quinn, J. M. Sauer, K. Powell, L. Ruslim, Z. Ren, F. Bard, T. A. Yednock, I. Griswold-Prenner
Design And Synthesis Of A Novel, Orally Active, Brain Penetrant, Tri-Substituted Thiophene Based Jnk Inhibitor.
Bioorg. Med. Chem. Lett. V. 21 1838 2011
PubMed-ID: 21316234 | Reference-DOI: 10.1016/J.BMCL.2011.01.046

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 10
	Chains	:	A
	EC Number	:	2.7.11.24
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	UNP RESIDUES 40-401
	Gene	:	MAPK10, JNK3, JNK3A, PRKM10
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	MAP KINASE 10, MAPK 10, MAP KINASE P49 3F12, STRESS- ACTIVATED PROTEIN KINASE JNK3, C-JUN N-TERMINAL KINASE 3

Molecule 2 - C-JUN-AMINO-TERMINAL KINASE-INTERACTING PROTEIN 1
	Chains	:	J
	Engineered	:	YES
	Fragment	:	UNP RESIDUES 157-167
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	JIP-1, JNK-INTERACTING PROTEIN 1, ISLET-BRAIN 1, IB-1, JNK MAP KINASE SCAFFOLD PROTEIN 1, MITOGEN-ACTIVATED PROTEIN KINASE 8- INTERACTING PROTEIN 1
	Synthetic	:	YES

		1	2
Asymmetric/Biological Unit	:	A	J

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	932	1	Ligand/Ion	N-[4-METHYL-3-(1H-1,2,4-TRIAZOL-5-YL)THIOPHEN-2-YL]-2-(2-OXO-3,4-DIHYDROQUINOLIN-1(2H)-YL)ACETAMIDE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:70 , VAL A:78 , ALA A:91 , MET A:146 , GLU A:147 , MET A:149 , ASP A:150 , ALA A:151 , ASN A:152 , VAL A:196 , HOH A:405	BINDING SITE FOR RESIDUE 932 A 1

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

Asymmetric/Biological Unit

No.	Residues
1	Phe A:208	-	Gly A:209
2	Gly A:209	-	Leu A:210
3	Leu A:210	-	Ala A:211
4	His A:324	-	Asn A:325
5	Lys A:326	-	Leu A:327
6	Leu A:327	-	Lys A:328
7	Gln A:379	-	Leu A:380
8	Asp A:381	-	Glu A:382

(no "SAP(SNP)/Variant" information available for 3PTG)

Asymmetric/Biological Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	MAPK	PS01351	MAP kinase signature.	MK10_HUMAN	99-201	1	A:99-201
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	MK10_HUMAN	185-197	1	A:185-197

Asymmetric/Biological Unit (11, 11)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000241014	1	ENSE00001182340	chr11:45907202-45907472	271	JIP1_HUMAN	1-34	34	0	-	-
1.3	ENST00000241014	3	ENSE00000824604	chr11:45919636-45919741	106	JIP1_HUMAN	34-69	36	0	-	-
1.4a	ENST00000241014	4a	ENSE00000824603	chr11:45921689-45922003	315	JIP1_HUMAN	70-174	105	1	J:154-163	10
1.5b	ENST00000241014	5b	ENSE00000824602	chr11:45923531-45923612	82	JIP1_HUMAN	175-202	28	0	-	-
1.6c	ENST00000241014	6c	ENSE00000824601	chr11:45923923-45924735	813	JIP1_HUMAN	202-473	272	0	-	-
1.7	ENST00000241014	7	ENSE00000824600	chr11:45924916-45924991	76	JIP1_HUMAN	473-498	26	0	-	-
1.8	ENST00000241014	8	ENSE00000824599	chr11:45925540-45925712	173	JIP1_HUMAN	498-556	59	0	-	-
1.9	ENST00000241014	9	ENSE00000824598	chr11:45926006-45926115	110	JIP1_HUMAN	556-592	37	0	-	-
1.10	ENST00000241014	10	ENSE00000824597	chr11:45926269-45926385	117	JIP1_HUMAN	593-631	39	0	-	-
1.11	ENST00000241014	11	ENSE00000824596	chr11:45926522-45926592	71	JIP1_HUMAN	632-655	24	0	-	-
1.12	ENST00000241014	12	ENSE00000824595	chr11:45926702-45926800	99	JIP1_HUMAN	655-688	34	0	-	-
1.13b	ENST00000241014	13b	ENSE00001522301	chr11:45927200-45928016	817	JIP1_HUMAN	688-711	24	0	-	-

2.6b	ENST00000395169	6b	ENSE00002029030	chr4:87281269-87280811	459	MK10_HUMAN	-	0	0	-	-
2.11c	ENST00000395169	11c	ENSE00001352600	chr4:87275797-87275683	115	MK10_HUMAN	-	0	0	-	-
2.14c	ENST00000395169	14c	ENSE00001520792	chr4:87115560-87115462	99	MK10_HUMAN	-	0	0	-	-
2.17d	ENST00000395169	17d	ENSE00002157878	chr4:87080620-87080451	170	MK10_HUMAN	1-41	41	0	-	-
2.19g	ENST00000395169	19g	ENSE00002201403	chr4:87028505-87028376	130	MK10_HUMAN	41-84	44	1	A:46-84	39
2.20b	ENST00000395169	20b	ENSE00001800335	chr4:87024397-87024339	59	MK10_HUMAN	85-104	20	1	A:85-104	20
2.21b	ENST00000395169	21b	ENSE00001654569	chr4:87023185-87023047	139	MK10_HUMAN	104-150	47	1	A:104-150	47
2.22b	ENST00000395169	22b	ENSE00001609893	chr4:87022370-87022205	166	MK10_HUMAN	151-206	56	1	A:151-206	56
2.23c	ENST00000395169	23c	ENSE00001789401	chr4:87019748-87019677	72	MK10_HUMAN	206-230	25	1	A:206-230 (gaps)	25
2.28b	ENST00000395169	28b	ENSE00000729500	chr4:86989108-86988926	183	MK10_HUMAN	230-291	62	1	A:230-291	62
2.29	ENST00000395169	29	ENSE00000729498	chr4:86985543-86985419	125	MK10_HUMAN	291-332	42	1	A:291-332 (gaps)	42
2.30	ENST00000395169	30	ENSE00001076721	chr4:86952584-86952521	64	MK10_HUMAN	333-354	22	1	A:333-354	22
2.31	ENST00000395169	31	ENSE00001218615	chr4:86950427-86950350	78	MK10_HUMAN	354-380	27	1	A:354-380	27
2.32h	ENST00000395169	32h	ENSE00001811960	chr4:86938523-86936276	2248	MK10_HUMAN	380-426	47	1	A:380-401	22

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:340
 aligned with MK10_HUMAN | P53779 from UniProtKB/Swiss-Prot  Length:464

    Alignment length:356
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395      
           MK10_HUMAN    46 NQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLARTAGTSFMMTPYVVTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPADSEHNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNS 401
               SCOP domains d3ptga_ A: c-jun N-terminal kinase (jnk3s)                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------Pkinase-3ptgA01 A:64-359                                                                                                                                                                                                                                                                                ------------------------------------------ Pfam domains
         Sec.struct. author ..eeee......eeee..eeeeeeee....eeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhh.........eeeee............eeeee...eehhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee......-------------.hhhhhhhhhhh......hhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhh...hhhhhhhh.......hhhhhhhhhhh..---....hhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh..hhhhhh................hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------MAPK  PDB: A:99-201 UniProt: 99-201                                                                    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------------------------------------------------------------------------------------------------PROTEIN_KINAS------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 2 (1) Exon 2.19g  PDB: A:46-84 UniProt: 41-84Exon 2.20b          ----------------------------------------------Exon 2.22b  PDB: A:151-206 UniProt: 151-206             -----------------------Exon 2.28b  PDB: A:230-291 UniProt: 230-291                   -----------------------------------------Exon 2.30             -------------------------Exon 2.32h             Transcript 2 (1)
           Transcript 2 (2) ----------------------------------------------------------Exon 2.21b  PDB: A:104-150 UniProt: 104-150    -------------------------------------------------------Exon 2.23c               ------------------------------------------------------------Exon 2.29  PDB: A:291-332 (gaps)          ---------------------Exon 2.31  PDB: A:354-380  --------------------- Transcript 2 (2)
                 3ptg A  46 NQFYSVEVGDSTFTVLKRYQNLKPIGSGAQGIVCAAYDAVLDRNVAIKKLSRPFQNQTHAKRAYRELVLMKCVNHKNIISLLNVFTPQKTLEEFQDVYLVMELMDANLCQVIQMELDHERMSYLLYQMLCGIKHLHSAGIIHRDLKPSNIVVKSDCTLKILDFGLA-------------VTRYYRAPEVILGMGYKENVDIWSVGCIMGEMVRHKILFPGRDYIDQWNKVIEQLGTPCPEFMKKLQPTVRNYVENRPKYAGLTFPKLFPDSLFPA---HNKLKASQARDLLSKMLVIDPAKRISVDDALQHPYINVWYDPAEVEAPPPQIYDKQLDEREHTIEEWKELIYKEVMNS 401
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205     |   -       225       235       245       255       265       275       285       295       305       315    |  325       335       345       355       365       375       385       395      
                                                                                                                                                                                               211           225                                                                                            320 324

Chain J from PDB  Type:PROTEIN  Length:10
 aligned with JIP1_HUMAN | Q9UQF2 from UniProtKB/Swiss-Prot  Length:711

    Alignment length:10
                                   167
           JIP1_HUMAN   158 PKRPTTLNLF 167
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
               Transcript 1 Exon 1.4a  Transcript 1
                 3ptg J 154 PKRPTTLNLF 163
                                   163

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: c-jun N-terminal kinase (jnk3s) (29)

Human (Homo sapiens) [TaxId: 9606] (29)

d3ptga_

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PKinase (934)

Family: Pkinase (680)

Homo sapiens (Human) (521)

Pkinase-3ptgA01

A:64-359

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MK10_HUMAN | P53779)

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:0004708	MAP kinase kinase activity	Catalysis of the concomitant phosphorylation of threonine (T) and tyrosine (Y) residues in a Thr-Glu-Tyr (TEY) thiolester sequence in a MAP kinase (MAPK) substrate.
	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:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	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: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: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:0009416	response to light stimulus	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 light stimulus, electromagnetic radiation of wavelengths classified as infrared, visible or ultraviolet light.
	GO:0048511	rhythmic process	Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
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:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Chain J (JIP1_HUMAN | Q9UQF2)

molecular function
	GO:0008432	JUN kinase binding	Interacting selectively and non-covalently with JUN kinase, an enzyme that catalyzes the phosphorylation and activation of members of the JUN family.
	GO:0005078	MAP-kinase scaffold activity	The binding activity of a molecule that functions as a physical support for the assembly of a multiprotein mitogen-activated protein kinase (MAPK) complex. Binds multiple kinases of the MAPKKK cascade, and also upstream signaling proteins, permitting those molecules to function in a coordinated way. Bringing together multiple enzymes and their substrates enables the signal to be transduced quickly and efficiently.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0019894	kinesin binding	Interacting selectively and non-covalently and stoichiometrically with kinesin, a member of a superfamily of microtubule-based motor proteins that perform force-generating tasks such as organelle transport and chromosome segregation.
	GO:0031434	mitogen-activated protein kinase kinase binding	Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase, any protein that can phosphorylate a MAP kinase.
	GO:0031435	mitogen-activated protein kinase kinase kinase binding	Interacting selectively and non-covalently with a mitogen-activated protein kinase kinase kinase, any protein that can phosphorylate a MAP kinase kinase.
	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:0019901	protein kinase binding	Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
	GO:0004860	protein kinase inhibitor activity	Stops, prevents or reduces the activity of a protein kinase, an enzyme which phosphorylates a protein.
biological process
	GO:0007258	JUN phosphorylation	The process of introducing a phosphate group into a JUN protein.
	GO:0046329	negative regulation of JNK cascade	Any process that stops, prevents, or reduces the frequency, rate or extent of signal transduction mediated by the JNK cascade.
	GO:0043508	negative regulation of JUN kinase activity	Any process that stops, prevents, or reduces the frequency, rate or extent of JUN kinase activity.
	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:2001243	negative regulation of intrinsic apoptotic signaling pathway	Any process that stops, prevents or reduces the frequency, rate or extent of intrinsic apoptotic signaling pathway.
	GO:0009967	positive regulation of signal transduction	Any process that activates or increases the frequency, rate or extent of signal transduction.
	GO:0046328	regulation of JNK cascade	Any process that modulates the frequency, rate or extent of signal transduction mediated by the JNK cascade.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
	GO:0016192	vesicle-mediated transport	A cellular transport process in which transported substances are moved in membrane-bounded vesicles; transported substances are enclosed in the vesicle lumen or located in the vesicle membrane. The process begins with a step that directs a substance to the forming vesicle, and includes vesicle budding and coating. Vesicles are then targeted to, and fuse with, an acceptor membrane.
cellular component
	GO:0030424	axon	The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
	GO:0044295	axonal growth cone	The migrating motile tip of a growing nerve cell axon.
	GO:0044297	cell body	The portion of a cell bearing surface projections such as axons, dendrites, cilia, or flagella that includes the nucleus, but excludes all cell projections.
	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:0030425	dendrite	A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
	GO:0044294	dendritic growth cone	The migrating motile tip of a growing nerve cell dendrite.
	GO:0044302	dentate gyrus mossy fiber	Distinctive, unmyelinated axons produced by granule cells.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031966	mitochondrial membrane	Either of the lipid bilayers that surround the mitochondrion and form the mitochondrial envelope.
	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:0043005	neuron projection	A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
	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:0048471	perinuclear region of cytoplasm	Cytoplasm situated near, or occurring around, the nucleus.
	GO:0045202	synapse	The junction between a nerve fiber of one neuron and another neuron, muscle fiber or glial cell. As the nerve fiber approaches the synapse it enlarges into a specialized structure, the presynaptic nerve ending, which contains mitochondria and synaptic vesicles. At the tip of the nerve ending is the presynaptic membrane; facing it, and separated from it by a minute cleft (the synaptic cleft) is a specialized area of membrane on the receiving cell, known as the postsynaptic membrane. In response to the arrival of nerve impulses, the presynaptic nerve ending secretes molecules of neurotransmitters into the synaptic cleft. These diffuse across the cleft and transmit the signal to the postsynaptic membrane.

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(no "Related Entries Specified in the PDB File" available for 3PTG)

Description

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