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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ACTIVATED (THR->ASP) POLO-LIKE KINASE 1 (PLK1) CATALYTIC DOMAIN IN COMPLEX WITH COMPOUND 257
 
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 :  3.35
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)

(-) Compounds

Molecule 1 - POLO-LIKE KINASE 1
    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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
12FR1Ligand/Ion3-[3-(3-METHYL-6-{[(1S)-1-PHENYLETHYL]AMINO}-1H-PYRAZOLO[4,3-C]PYRIDIN-1-YL)PHENYL]PROPANAMIDE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:45 , GLY A:48 , CYS A:53 , LEU A:116 , GLU A:117 , CYS A:119 , ARG A:122 , GLY A:166 , PHE A:169BINDING SITE FOR RESIDUE 2FR A 313

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DBC)

(-) Sequences/Alignments

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 3dbcA01 A:24-119 Phosphorylase Kinase; domain 1                                                 3dbcA02 A:120-310 Transferase(Phosphotransferase) domain 1                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee......eeeeeeeeeee..eeeeeeee.....eeeeeeee.hhh...hhhhhhhhhhhhhhhh.......eeeeee...eeeeee......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee.--------------------------..hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh.......hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dbc 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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3DBC)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        Q4KMI8_DANRE | Q4KMI8: 3d5u 3d5v
UniProtKB/TrEMBL
        Q4KMI8_DANRE | Q4KMI8: 3d5w 3d5x 3db6 3db8 3dbd 3dbe 3dbf

(-) Related Entries Specified in the PDB File

3d5w 3db6 3db8 3dbd 3dbe 3dbf