4E4N - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   JAK1 KINASE (JH1 DOMAIN) IN COMPLEX WITH COMPOUND 49

Authors :   C. Eigenbrot

Date :   13 Mar 12 (Deposition) - 30 May 12 (Release) - 11 Jul 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   O-Phosphotyrosine, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. J. Kulagowski, W. Blair, R. J. Bull, C. Chang, G. Deshmukh, H. J. Dyke C. Eigenbrot, N. Ghilardi, P. Gibbons, T. K. Harrison, P. R. Hewitt, M. Liimatta, C. A. Hurley, A. Johnson, T. Johnson, J. R. Kenny, P. Bir Kohli, R. J. Maxey, R. Mendonca, K. Mortara, J. Murray, R. Narukulla, S. Shia, M. Steffek, S. Ubhayakar, M. Ultsch, A. Van Abbema, S. I. Ward, B. Waszkowycz, M. Zak
Identification Of Imidazo-Pyrrolopyridines As Novel And Potent Jak1 Inhibitors.
J. Med. Chem. V. 55 5901 2012
PubMed-ID: 22591402 | Reference-DOI: 10.1021/JM300438J

Molecule 1 - TYROSINE-PROTEIN KINASE JAK1
	Chains	:	A, B
	EC Number	:	2.7.10.2
	Engineered	:	YES
	Expression System	:	SPODOPTERA FRUGIPERDA
	Expression System Common	:	FALL ARMYWORM
	Expression System Taxid	:	7108
	Fragment	:	PROTEIN KINASE DOMAIN JH1, UNP RESIDUES 854-1154
	Gene	:	JAK1, JAK1A, JAK1B
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	JANUS KINASE 1, JAK-1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	0NL	2	Ligand/Ion	TERT-BUTYL [(1R,3R)-3-(IMIDAZO[4,5-D]PYRROLO[2,3-B]PYRIDIN-1(6H)-YL)CYCLOPENTYL]CARBAMATE
2	PTR	4	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	0NL	1	Ligand/Ion	TERT-BUTYL [(1R,3R)-3-(IMIDAZO[4,5-D]PYRROLO[2,3-B]PYRIDIN-1(6H)-YL)CYCLOPENTYL]CARBAMATE
2	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	0NL	1	Ligand/Ion	TERT-BUTYL [(1R,3R)-3-(IMIDAZO[4,5-D]PYRROLO[2,3-B]PYRIDIN-1(6H)-YL)CYCLOPENTYL]CARBAMATE
2	PTR	2	Mod. Amino Acid	O-PHOSPHOTYROSINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:882 , GLU A:883 , GLY A:887 , LYS A:888 , VAL A:889 , ALA A:906 , LYS A:908 , MET A:956 , GLU A:957 , PHE A:958 , LEU A:959 , ASN A:1008 , LEU A:1010 , GLY A:1020 , ASP A:1021 , HOH A:1393	BINDING SITE FOR RESIDUE 0NL A 1201
2	AC2	SOFTWARE	GLY B:882 , GLU B:883 , GLY B:884 , GLY B:887 , VAL B:889 , ALA B:906 , LYS B:908 , GLU B:957 , PHE B:958 , LEU B:959 , ASN B:1008 , LEU B:1010 , ASP B:1021 , HOH B:1315 , HOH B:1447	BINDING SITE FOR RESIDUE 0NL B 1201

(no "SS Bond" information available for 4E4N)

(no "Cis Peptide Bond" information available for 4E4N)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041715	N	973	K	JAK1_HUMAN	Polymorphism	34680086	A/B	N	973	K

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_041715	N	973	K	JAK1_HUMAN	Polymorphism	34680086	A	N	973	K

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_041715	N	973	K	JAK1_HUMAN	Polymorphism	34680086	B	N	973	K

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	JAK1_HUMAN	881-908	2	A:881-908 B:881-908
2	PROTEIN_KINASE_TYR	PS00109	Tyrosine protein kinases specific active-site signature.	JAK1_HUMAN	999-1011	2	A:999-1011 B:999-1011

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.	JAK1_HUMAN	881-908	1	A:881-908 -
2	PROTEIN_KINASE_TYR	PS00109	Tyrosine protein kinases specific active-site signature.	JAK1_HUMAN	999-1011	1	A:999-1011 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PROTEIN_KINASE_ATP	PS00107	Protein kinases ATP-binding region signature.	JAK1_HUMAN	881-908	1	- B:881-908
2	PROTEIN_KINASE_TYR	PS00109	Tyrosine protein kinases specific active-site signature.	JAK1_HUMAN	999-1011	1	- B:999-1011

(no "Exon" information available for 4E4N)

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:293
 aligned with JAK1_HUMAN | P23458 from UniProtKB/Swiss-Prot  Length:1154

    Alignment length:302
                                   862       872       882       892       902       912       922       932       942       952       962       972       982       992      1002      1012      1022      1032      1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152  
          JAK1_HUMAN    853 PDIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK 1154
               SCOP domains d4e4na_ A: automated matches                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhh.eeeeeeeee...eeeeeeee........eeeeeeee..-----.hhhhhhhhhhhhh........eeeee..----..eeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee......eee.......hhhhhhhhhhhhheeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------PROTEIN_KINASE_ATP          ------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4e4n A  853 GDIVSEKKPATEVDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKP-----HIADLKKEIEILRNLYHENIVKYKGICTE----GIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEyyTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK 1154
                                   862       872       882       892       902       912     | 922       932       942   |   952       962       972       982       992      1002      1012      1022      1032 ||   1042      1052      1062      1072      1082      1092      1102      1112      1122      1132      1142      1152  
                                                                                     912   918                         946  951                                                                               1034-PTR                                                                                                                    
                                                                                                                                                                                                               1035-PTR

Chain B from PDB  Type:PROTEIN  Length:282
 aligned with JAK1_HUMAN | P23458 from UniProtKB/Swiss-Prot  Length:1154

    Alignment length:290
                                   874       884       894       904       914       924       934       944       954       964       974       984       994      1004      1014      1024      1034      1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154
          JAK1_HUMAN    865 VDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKPESGGNHIADLKKEIEILRNLYHENIVKYKGICTEDGGNGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEYYTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK 1154
               SCOP domains d4e4nb_ B: automated matches                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhh.eeeeeeeee...eeeeeeee........eeeeeeee..----.hhhhhhhhhhhhhh........eeeee.----...eeeee.....hhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eeeee..eeee......ee......eee.......hhhhhhhhhhhhheeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..........hhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------K------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------PROTEIN_KINASE_ATP          ------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4e4n B  865 VDPTHFEKRFLKRIRDLGEGHFGKVELCRYDPEGDNTGEQVAVKSLKP----NHIADLKKEIEILRNLYHENIVKYKGICT----NGIKLIMEFLPSGSLKEYLPKNKNKINLKQQLKYAVQICKGMDYLGSRQYVHRDLAARNVLVESEHQVKIGDFGLTKAIETDKEyyTVKDDRDSPVFWYAPECLMQSKFYIASDVWSFGVTLHELLTYCDSDSSPMALFLKMIGPTHGQMTVTRLVNTLKEGKRLPCPPNCPDEVYQLMRKCWEFQPSNRTSFQNLIEGFEALLK 1154
                                   874       884       894       904       | -  |    924       934       944|    | 954       964       974       984       994      1004      1014      1024      1034|     1044      1054      1064      1074      1084      1094      1104      1114      1124      1134      1144      1154
                                                                         912  917                         945  950                                                                                1034-PTR                                                                                                                    
                                                                                                                                                                                                   1035-PTR

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)

1a	d4e4na_	A:
1b	d4e4nb_	B:

(no "CATH Domain" information available for 4E4N)

(no "Pfam Domain" information available for 4E4N)

Asymmetric Unit(hide GO term definitions)

Chain A,B (JAK1_HUMAN | P23458)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0031730	CCR5 chemokine receptor binding	Interacting selectively and non-covalently with a CCR5 chemokine receptor.
	GO:0005088	Ras guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0005131	growth hormone receptor binding	Interacting selectively and non-covalently with the growth hormone receptor.
	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:0004715	non-membrane spanning protein tyrosine kinase activity	Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
	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:0004713	protein tyrosine kinase activity	Catalysis of the reaction: ATP + a protein tyrosine = ADP + protein tyrosine phosphate.
	GO:0005102	receptor binding	Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
	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.
	GO:0031625	ubiquitin protein ligase binding	Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
	GO:0000165	MAPK cascade	An intracellular protein kinase cascade containing at least a MAPK, a MAPKK and 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:0030154	cell differentiation	The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
	GO:0016477	cell migration	The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
	GO:0045087	innate immune response	Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
	GO:0060333	interferon-gamma-mediated signaling pathway	A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
	GO:0038110	interleukin-2-mediated signaling pathway	A series of molecular signals initiated by the binding of interleukin-2 to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0035556	intracellular signal transduction	The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
	GO:0038083	peptidyl-tyrosine autophosphorylation	The phosphorylation by a protein of one or more of its own tyrosine amino acid residues, or a tyrosine residue on an identical protein.
	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:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:1903672	positive regulation of sprouting angiogenesis	Any process that activates or increases the frequency, rate or extent of sprouting angiogenesis.
	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:0042127	regulation of cell proliferation	Any process that modulates the frequency, rate or extent of cell proliferation.
	GO:0060334	regulation of interferon-gamma-mediated signaling pathway	Any process that modulates the rate, frequency or extent of the series of molecular events generated as a consequence of interferon-gamma binding to a cell surface receptor.
	GO:0060338	regulation of type I interferon-mediated signaling pathway	Any process that modulates the rate, frequency or extent of a type I interferon-mediated signaling pathway. A type I interferon-mediated signaling pathway is the series of molecular events generated as a consequence of a type I interferon binding to a cell surface receptor.
	GO:0046677	response to antibiotic	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 antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	GO:0007169	transmembrane receptor protein tyrosine kinase signaling pathway	A series of molecular signals initiated by the binding of an extracellular ligand to a receptor on the surface of the target cell where the receptor possesses tyrosine kinase activity, and ending with regulation of a downstream cellular process, e.g. transcription.
	GO:0060337	type I interferon signaling pathway	A series of molecular signals initiated by the binding of a type I interferon to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
cellular component
	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:0012505	endomembrane system	A collection of membranous structures involved in transport within the cell. The main components of the endomembrane system are endoplasmic reticulum, Golgi bodies, vesicles, cell membrane and nuclear envelope. Members of the endomembrane system pass materials through each other or though the use of vesicles.
	GO:0031234	extrinsic component of cytoplasmic side of plasma membrane	The component of a plasma membrane consisting of gene products and protein complexes that are loosely bound to its cytoplasmic surface, but not integrated into the hydrophobic region.
	GO:0005925	focal adhesion	Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	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.

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	4e4n
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Description

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Ligands, Modified Residues, Ions (2, 6)

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