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(-) Description

Title :  STRUCTURE GUIDED DEVELOPMENT OF NOVEL THYMIDINE MIMETICS TARGETING PSEUDOMONAS AERUGINOSA THYMIDYLATE KINASE: FROM HIT TO LEAD GENERATION
 
Authors :  J. Y. Choi, M. S. Plummer, J. Starr, C. R. Desbonnet, H. H. Soutter, J. Cha J. R. Miller, K. Dillman, A. A. Miller, W. R. Roush
Date :  02 Dec 11  (Deposition) - 01 Feb 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Thymidylate Kinase, Kinase, Thymidine Triphosphate, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Y. Choi, M. S. Plummer, J. Starr, C. R. Desbonnet, H. Soutter, J. Chang, J. R. Miller, K. Dillman, A. A. Miller, W. R. Roush
Structure Guided Development Of Novel Thymidine Mimetics Targeting Pseudomonas Aeruginosa Thymidylate Kinase: From Hit To Lead Generation.
J. Med. Chem. V. 55 852 2012
PubMed-ID: 22243413  |  Reference-DOI: 10.1021/JM201349F

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    ChainsA, B
    EC Number2.7.4.9
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15B
    Expression System StrainBL21 DE3
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentKINASE DOMAIN
    GenePA2962, TMK
    Organism ScientificPSEUDOMONAS AERUGINOSA
    Organism Taxid208964
    StrainATCC 15692 / PAO1 / 1C / PRS 101 / LMG 12228
    SynonymDTMP KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
10DJ2Ligand/Ion3-(1-METHYL-2-OXO-2,3-DIHYDRO-1H-IMIDAZO[4,5-B]PYRIDIN-6-YL)BENZAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
10DJ1Ligand/Ion3-(1-METHYL-2-OXO-2,3-DIHYDRO-1H-IMIDAZO[4,5-B]PYRIDIN-6-YL)BENZAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
10DJ1Ligand/Ion3-(1-METHYL-2-OXO-2,3-DIHYDRO-1H-IMIDAZO[4,5-B]PYRIDIN-6-YL)BENZAMIDE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
10DJ2Ligand/Ion3-(1-METHYL-2-OXO-2,3-DIHYDRO-1H-IMIDAZO[4,5-B]PYRIDIN-6-YL)BENZAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:12 , GLU A:39 , MET A:70 , ARG A:74 , ARG A:96 , ALA A:100 , THR A:101 , TYR A:104 , GLN A:105 , PHE A:155 , PHE A:163 , HOH A:244 , HOH A:290 , HOH A:307BINDING SITE FOR RESIDUE 0DJ A 800
2AC2SOFTWAREGLU B:39 , PRO B:40 , MET B:70 , ARG B:74 , ARG B:96 , ALA B:100 , THR B:101 , TYR B:104 , GLN B:105 , PHE B:155 , PHE B:163 , HOH B:224BINDING SITE FOR RESIDUE 0DJ B 801

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Glu A:39 -Pro A:40
2Glu B:39 -Pro B:40

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3UWO)

(-) Sequences/Alignments

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:194
 aligned with KTHY_PSEAE | Q9HZN8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:205
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202     
           KTHY_PSEAE     3 GLFVTLEGPEGAGKSTNRDYLAERLRERGIEVQLTREPGGTPLAERIRELLLAPSDEPMAADTELLLMFAARAQHLAGVIRPALARGAVVLCDRFTDATYAYQGGGRGLPEARIAALESFVQGDLRPDLTLVFDLPVEIGLARAAARGRLDRFEQEDRRFFEAVRQTYLQRAAQAPERYQVLDAGLPLAEVQAGLDRLLPNLLER 207
               SCOP domains d3uwoa_ A: automated matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee...-----------........hhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uwo A   3 GLFVTLEGPEGAGKSTNRDYLAERLRERGIEVQLTREPGGTPLAERIRELLLAPSDEPMAADTELLLMFAARAQHLAGVIRPALARGAVVLCDRFTDATYAYQGGGRGLPEARIAALESFVQGDLRPDLTLVFDLPV-----------RLDRFEQEDRRFFEAVRQTYLQRAAQAPERYQVLDAGLPLAEVQAGLDRLLPNLLER 207
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      |  -       152       162       172       182       192       202     
                                                                                                                                                                  139         151                                                        

Chain B from PDB  Type:PROTEIN  Length:191
 aligned with KTHY_PSEAE | Q9HZN8 from UniProtKB/Swiss-Prot  Length:210

    Alignment length:203
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202   
           KTHY_PSEAE     3 GLFVTLEGPEGAGKSTNRDYLAERLRERGIEVQLTREPGGTPLAERIRELLLAPSDEPMAADTELLLMFAARAQHLAGVIRPALARGAVVLCDRFTDATYAYQGGGRGLPEARIAALESFVQGDLRPDLTLVFDLPVEIGLARAAARGRLDRFEQEDRRFFEAVRQTYLQRAAQAPERYQVLDAGLPLAEVQAGLDRLLPNLL 205
               SCOP domains d3uwob_ B: automated matches                                                                                                                                                                                SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee...------------.......hhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uwo B   3 GLFVTLEGPEGAGKSTNRDYLAERLRERGIEVQLTREPGGTPLAERIRELLLAPSDEPMAADTELLLMFAARAQHLAGVIRPALARGAVVLCDRFTDATYAYQGGGRGLPEARIAALESFVQGDLRPDLTLVFDLPV------------LDRFEQEDRRFFEAVRQTYLQRAAQAPERYQVLDAGLPLAEVQAGLDRLLPNLL 205
                                    12        22        32        42        52        62        72        82        92       102       112       122       132      |  -       152       162       172       182       192       202   
                                                                                                                                                                  139          152                                                     

   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  (1, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (KTHY_PSEAE | Q9HZN8)
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:0004798    thymidylate kinase activity    Catalysis of the reaction: ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate.
    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:0009041    uridylate kinase activity    Catalysis of the reaction: ATP + (d)UMP = ADP + (d)UDP.
biological process
    GO:0006233    dTDP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTDP, deoxyribosylthymine diphosphate (2'-deoxyribosylthymine5'-diphosphate).
    GO:0006235    dTTP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
    GO:0006227    dUDP biosynthetic process    The chemical reactions and pathways resulting in the formation of dUDP, deoxyuridine diphosphate (2'-deoxy-5'-uridylyl phosphate).
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    GO:0046939    nucleotide phosphorylation    The process of introducing one or more phosphate groups into a nucleotide to produce a phosphorylated nucleoside.
    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.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KTHY_PSEAE | Q9HZN83uwk 3uxm 4e5u 4edh 4esh 4gmd

(-) Related Entries Specified in the PDB File

3uwk 3uxm