2VAG - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF DI-PHOSPHORYLATED HUMAN CLK1 IN COMPLEX WITH A NOVEL SUBSTITUTED INDOLE INHIBITOR

Authors :   A. C. W. Pike, A. N. Bullock, O. Fedorov, E. S. Pilka, E. Ugochukwu, F. Von A. Edwards, C. H. Arrowsmith, J. Weigelt, M. Sundstrom, K. Huber, F. Br S. Knapp

Date :   31 Aug 07 (Deposition) - 09 Oct 07 (Release) - 07 Dec 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym./Biol. Unit : A

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

Reference :   O. Fedorov, K. Huber, A. Eisenreich, P. Filippakopoulos, O. King, A. N. Bullock, D. Szklarczyk, L. J. Jensen, D. Fabbro, J. Trappe, U. Rauch, F. Bracher, S. Knapp
Specific Clk Inhibitors From A Novel Chemotype For Regulation Of Alternative Splicing.
Chem. Biol V. 18 67 2011
PubMed-ID: 21276940 | Reference-DOI: 10.1016/J.CHEMBIOL.2010.11.009

Molecule 1 - DUAL SPECIFICITY PROTEIN KINASE CLK1
	Chains	:	A
	EC Number	:	2.7.12.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PLIC-SGC1
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Expression System Variant	:	R3
	Fragment	:	KINASE DOMAIN, RESIDUES 148-484
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	CDC-LIKE KINASE 1

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	SEP	1	Mod. Amino Acid	PHOSPHOSERINE
2	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE
3	V25	1	Ligand/Ion	ETHYL 3-[(E)-2-AMINO-1-CYANOETHENYL]-6,7-DICHLORO-1-METHYL-1H-INDOLE-2-CARBOXYLATE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:167 , GLY A:168 , GLU A:169 , VAL A:175 , ALA A:189 , LYS A:191 , PHE A:241 , GLU A:242 , GLU A:292 , ASN A:293 , LEU A:295 , VAL A:324	BINDING SITE FOR RESIDUE V25 A1482

(no "SS Bond" information available for 2VAG)

(no "Cis Peptide Bond" information available for 2VAG)

Asymmetric/Biological Unit (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_040412	M	440	T	CLK1_HUMAN	Polymorphism	35393352	A	M	440	T
2	UniProt	VAR_051620	E	459	G	CLK1_HUMAN	Polymorphism	12709	A	E	459	G

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.	CLK1_HUMAN	167-191	1	A:167-191
2	PROTEIN_KINASE_ST	PS00108	Serine/Threonine protein kinases active-site signature.	CLK1_HUMAN	284-296	1	A:284-296

Asymmetric/Biological Unit (10, 10)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1a	ENST00000321356	1a	ENSE00001464368	chr2:201729422-201729287	136	CLK1_HUMAN	-	0	0	-	-
1.3a	ENST00000321356	3a	ENSE00002169022	chr2:201726585-201726425	161	CLK1_HUMAN	1-54	54	0	-	-
1.3c	ENST00000321356	3c	ENSE00002196398	chr2:201726189-201725961	229	CLK1_HUMAN	54-130	77	0	-	-
1.3i	ENST00000321356	3i	ENSE00001664086	chr2:201724938-201724848	91	CLK1_HUMAN	131-161	31	1	A:0-161	15
1.3k	ENST00000321356	3k	ENSE00001608435	chr2:201724469-201724403	67	CLK1_HUMAN	161-183	23	1	A:161-183	23
1.4b	ENST00000321356	4b	ENSE00001663450	chr2:201722812-201722696	117	CLK1_HUMAN	183-222	40	1	A:183-222	40
1.5a	ENST00000321356	5a	ENSE00001792660	chr2:201722607-201722441	167	CLK1_HUMAN	222-278	57	1	A:222-278	57
1.5c	ENST00000321356	5c	ENSE00001606598	chr2:201721708-201721614	95	CLK1_HUMAN	278-309	32	1	A:278-306	29
1.6	ENST00000321356	6	ENSE00001599503	chr2:201721534-201721405	130	CLK1_HUMAN	310-353	44	1	A:310-353	44
1.7	ENST00000321356	7	ENSE00001686268	chr2:201719809-201719727	83	CLK1_HUMAN	353-380	28	1	A:353-380	28
1.8b	ENST00000321356	8b	ENSE00001653001	chr2:201719418-201719339	80	CLK1_HUMAN	381-407	27	1	A:381-407	27
1.9d	ENST00000321356	9d	ENSE00001782254	chr2:201718716-201718626	91	CLK1_HUMAN	407-437	31	1	A:407-437	31
1.10k	ENST00000321356	10k	ENSE00001823451	chr2:201718172-201717732	441	CLK1_HUMAN	438-484	47	1	A:438-481	44

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:332
 aligned with CLK1_HUMAN | P49759 from UniProtKB/Swiss-Prot  Length:484

    Alignment length:335
                                   156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476     
           CLK1_HUMAN   147 GHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYNPKIKRDERTLINPDIKVVDFGSATYDDEHHSTLVSTRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRRCKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLK 481
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2vagA01 A:0-220,A:225-243 Phosphorylase Kinase; domain 1                  2vag2vagA01            2vagA02 A:221-224,A:244-481 Transferase(Phosphotransferase) dom   ain 1                                                                                                                                                                        CATH domains
               Pfam domains --------------Pkinase-2vagA01 A:161-477                                                                                                                                                                                                                                                                                                    ---- Pfam domains
         Sec.struct. author hhhhh....ee...eeeeeeeeee..eeeeeeee......eeeeeee..hhhhhhhhhhhhhhhhhhhhhh.........eeeeeee..eeeeeee....hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee....eeeee.---..eeeee....eee......ee...............hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhhhh.hhh.ee..ee.....hhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T------------------G---------------------- SAPs(SNPs)
                    PROSITE --------------------PROTEIN_KINASE_ATP       --------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3i      ---------------------Exon 1.4b  PDB: A:183-222               -------------------------------------------------------Exon 1.5c  PDB: A:278-306       Exon 1.6  PDB: A:310-353 UniProt: 310-353   ---------------------------Exon 1.8b  PDB: A:381-407  ------------------------------Exon 1.10k  PDB: A:438-481 UniProt: 438-484  Transcript 1 (1)
           Transcript 1 (2) --------------Exon 1.3k              --------------------------------------Exon 1.5a  PDB: A:222-278 UniProt: 222-278               --------------------------------------------------------------------------Exon 1.7  PDB: A:353-380    --------------------------Exon 1.9d  PDB: A:407-437      -------------------------------------------- Transcript 1 (2)
                 2vag A   0 MHLICQSGDVLSARYEIVDTLGEGAFGKVVECIDHKAGGRHVAVKIVKNVDRYCEAARSEIQVLEHLNTTDPNSTFRCVQMLEWFEHHGHICIVFELLGLSTYDFIKENGFLPFRLDHIRKMAYQICKSVNFLHSNKLTHTDLKPENILFVQSDYTEAYN---KRDERTLINPDIKVVDFGSATYDDEHHSTLVstRHYRAPEVILALGWSQPCDVWSIGCILIEYYLGFTVFPTHDSKEHLAMMERILGPLPKHMIQKTRKRKYFHHDRLDWDEHSSAGRYVSRACKPLKEFMLSQDVEHERLFDLIQKMLEYDPAKRITLREALKHPFFDLLK 481
                            ||     156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306   |   316       326       336    || 346       356       366       376       386       396       406       416       426       436       446       456       466       476     
                            ||                                                                                                                                                           306 310                            341-SEP                                                                                                                                        
                            0|                                                                                                                                                                                               342-TPO                                                                                                                                       
                           148

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 '\|'

(no "SCOP Domain" information available for 2VAG)

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

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)

2vagA01

A:0-220,A:225-243

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)

2vagA02

A:221-224,A:244-481

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PKinase (934)

Family: Pkinase (680)

Homo sapiens (Human) (521)

Pkinase-2vagA01

A:161-477

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (CLK1_HUMAN | P49759)

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: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: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:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	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: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: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:0043484	regulation of RNA splicing	Any process that modulates the frequency, rate or extent of RNA splicing, the process of removing sections of the primary RNA transcript to remove sequences not present in the mature form of the RNA and joining the remaining sections to form the mature form of the RNA.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	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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	2vag
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	CLK1_HUMAN \| P49759
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	2.7.12.1
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	CLK1_HUMAN \| P49759
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UniProtKB/Swiss-Prot
	CLK1_HUMAN \| P49759	:	1z57 5j1v 5j1w

1z57	CRYSTAL STRUCTURE OF HUMAN CLK1 IN COMPLEX WITH 10Z-HYMENIALDISINE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 2)

PROSITE Motifs (2, 2)

Exons (10, 10)

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