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Title :   CRYSTAL STRUCTURE OF AN ACTIVATED (THR->ASP) POLO-LIKE KINASE 1 (PLK1) CATALYTIC DOMAIN IN COMPLEX WITH COMPOUND 562

Authors :   R. A. Elling, J. Zhu, K. J. Barr, M. J. Romanowski

Date :   31 May 08 (Deposition) - 07 Oct 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.20

Chains :   Asym./Biol. Unit : A

Keywords :   Polo-Like Kinase 1, Plk1, Catalytic Domain, Small-Molecule Inhibitor, Kinase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. V. Fucini, E. J. Hanan, M. J. Romanowski, R. A. Elling, W. Lew, K. J. Barr, J. Zhu, J. C. Yoburn, Y. Liu, B. T. Fahr, J. Fan, Y. Lu, P. Pham, I. C. Choong, E. C. Vanderporten, M. Bui, H. E. Purkey, M. J. Evanchik, W. Yang
Design And Synthesis Of 2-Amino-Pyrazolopyridines As Polo-Like Kinase 1 Inhibitors.
Bioorg. Med. Chem. Lett. V. 18 5648 2008
PubMed-ID: 18793847 | Reference-DOI: 10.1016/J.BMCL.2008.08.095
(for further references see the PDB file header)

Molecule 1 - POLO-LIKE KINASE
	Chains	:	A
	EC Number	:	2.7.11.21
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX6P-1
	Expression System Strain	:	BL21(DE3) STAR CODON+
	Expression System Vector Type	:	PLASMID
	Fragment	:	PLK1 KINASE DOMAIN
	Gene	:	PLK1
	Mutation	:	YES
	Organism Common	:	ZEBRAFISH
	Organism Scientific	:	DANIO RERIO
	Organism Taxid	:	7955

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	5FR	1	Ligand/Ion	4-({1-[3-(3-AMINO-3-OXOPROPYL)-5-CHLOROPHENYL]-3-METHYL-1H-PYRAZOLO[4,3-C]PYRIDIN-6-YL}AMINO)-3-METHOXY-N-(1-METHYLPIPERIDIN-4-YL)BENZAMIDE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:43 , LEU A:45 , LYS A:47 , CYS A:53 , ALA A:66 , GLU A:117 , CYS A:119 , ARG A:120 , ARG A:122 , PHE A:169	BINDING SITE FOR RESIDUE 5FR A 1

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

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

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

(no "PROSITE Motif" information available for 3DBF)

(no "Exon" information available for 3DBF)

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:261
 aligned with Q4KMI8_DANRE | Q4KMI8 from UniProtKB/TrEMBL  Length:595

    Alignment length:287
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
         Q4KMI8_DANRE    24 KEIPDVLVDPRTMKRYMRGRFLGKGGFAKCYEITDMDTKEVFAGKVVPKSMLLKPHQKEKMSTEIAIHKSLDNPHVVGFHGFFEDDDFVYVVLEICRRRSLLELHKRRKAVTEPEARYFMRQTIQGVQYLHNNRVIHRDLKLGNLFLNDDMDVKIGDFGLATKIEFDGERKKTLCGTPNYIAPEVLCKKGHSFEVDIWSLGCILYTLLVGKPPFETSCLKETYIRIKKNEYSVPRHINPVASALIRRMLHADPTLRPSVAELLTDEFFTSGYAPMRLPTSCLTVPPR 310
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dbfA01 A:24-119 Phosphorylase Kinase; domain 1                                                 3dbfA02 A:120-310 Transferase(Phosphotransferase) domain 1                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee........eeeeeeeeee..eeeeeeee.....eeeeeeee.......hhhhhhhhhhhhhhh........eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.--------------------------.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh.......hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dbf A  24 KEIPDVLVDPRTMKRYMRGRFLGKGGFAKCYEITDMDTKEVFAGKVVPKSMLLKPHQKEKMSTEIAIHKSLDNPHVVGFHGFFEDDDFVYVVLEICRRRSLLELHKRRKAVTEPEARYFMRQTIQGVQYLHNNRVIHRDLKLGNLFLNDDMDVKIGDFGLATKI--------------------------HSFEVDIWSLGCILYTLLVGKPPFETSCLKETYIRIKKNEYSVPRHINPVASALIRRMLHADPTLRPSVAELLTDEFFTSGYAPMRLPTSCLTVPPR 310
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183   |     -         -         -|      223       233       243       253       263       273       283       293       303       
                                                                                                                                                                                             187                        214

Chain A from PDB  Type:PROTEIN  Length:261
 aligned with Q6DRK7_DANRE | Q6DRK7 from UniProtKB/TrEMBL  Length:595

    Alignment length:287
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
         Q6DRK7_DANRE    24 KEIPDVLVDPRTMKRYMRGRFLGKGGFAKCYEITDMDTKEVFAGKVVPKSMLLKPHQKEKMSTEIAIHKSLDNPHVVGFHGFFEDDDFVYVVLEICRRRSLLELHKRRKAVTEPEARYFMRQTIQGVQYLHNNRVIHRDLKLGNLFLNDDMDVKIGDFGLATKIEFDGERKKTLCGTPNYIAPEVLCKKGHSFEVDIWSLGCILYTLLVGKPPFETSCLKETYIRIKKNEYSVPRHINPVASALIRRMLHADPTLRPSVAELLTDEFFTSGYAPMRLPTSCLTVPPR 310
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3dbfA01 A:24-119 Phosphorylase Kinase; domain 1                                                 3dbfA02 A:120-310 Transferase(Phosphotransferase) domain 1                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee........eeeeeeeeee..eeeeeeee.....eeeeeeee.......hhhhhhhhhhhhhhh........eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.--------------------------.hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh.......hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dbf A  24 KEIPDVLVDPRTMKRYMRGRFLGKGGFAKCYEITDMDTKEVFAGKVVPKSMLLKPHQKEKMSTEIAIHKSLDNPHVVGFHGFFEDDDFVYVVLEICRRRSLLELHKRRKAVTEPEARYFMRQTIQGVQYLHNNRVIHRDLKLGNLFLNDDMDVKIGDFGLATKI--------------------------HSFEVDIWSLGCILYTLLVGKPPFETSCLKETYIRIKKNEYSVPRHINPVASALIRRMLHADPTLRPSVAELLTDEFFTSGYAPMRLPTSCLTVPPR 310
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183   |     -         -         -|      223       233       243       253       263       273       283       293       303       
                                                                                                                                                                                             187                        214

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 3DBF)

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)

Zebrafish (Danio rerio) (4)

3dbfA01

A:24-119

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

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

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

Zebrafish (Danio rerio) (4)

3dbfA02

A:120-310

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q6DRK7_DANRE | Q6DRK7)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO: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:0000278	mitotic cell cycle	Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
	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.

Chain A (Q4KMI8_DANRE | Q4KMI8)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO: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:0000278	mitotic cell cycle	Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
	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.

Asymmetric/Biological Unit
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Description

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Ligands, Modified Residues, Ions (1, 1)

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