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(-) Description

Title :  SULFONYLPIPERIDINES AS NOVEL, ANTIBACTERIAL INHIBITORS OF GRAM-POSITIVE THYMIDYLATE KINASE (TMK): COMPOUND 5
 
Authors :  A. Boriack-Sjodin, N. Olivier
Date :  16 Oct 12  (Deposition) - 31 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tmk, Kinase, Thymidylate Kinase, Mrsa, Pipiridine, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Martinez-Botella, J. T. Loch, O. M. Green, S. P. Kawatkar, N. B. Olivier, P. A. Boriack-Sjodin, T. A. Keating
Sulfonylpiperidines As Novel, Antibacterial Inhibitors Of Gram-Positive Thymidylate Kinase (Tmk).
Bioorg. Med. Chem. Lett. V. 23 169 2013
PubMed-ID: 23206863  |  Reference-DOI: 10.1016/J.BMCL.2012.10.128

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30
    Expression System Strain: BL21 (DE3) CODON +
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: TMK
    Gene: SAR0483, TMK
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 282458
    Strain: MRSA252
    Synonym: DTMP KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1T052Ligand/Ion4-{[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]SULFONYL}-2-(3-METHYLPHENOXY)BENZOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:37 , ARG A:48 , LEU A:52 , PHE A:66 , SER A:69 , ARG A:70 , ARG A:92 , SER A:97 , TYR A:100 , GLN A:101 , HOH A:420 , HIS B:172 , SER B:175 , HOH B:477BINDING SITE FOR RESIDUE T05 A 301
2AC2SOFTWAREGLU B:37 , ARG B:48 , PHE B:66 , SER B:69 , ARG B:70 , ARG B:92 , SER B:97 , TYR B:100 , GLN B:101 , HOH B:452 , HOH B:460 , HOH B:472BINDING SITE FOR RESIDUE T05 B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:37 -Pro A:38
2Glu B:37 -Pro B:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HLC)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HLC)

(-) Exons   (0, 0)

(no "Exon" information available for 4HLC)

(-) 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:195
                                                                                                                                                                                                                                   
               SCOP domains d4hlca_ A: automated matches                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hlc A   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKLDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLE 203
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  ||   158       168       178       188       198     
                                                                                                                                                                        144|                                                   
                                                                                                                                                                         152                                                   


Chain B from PDB  Type:PROTEIN  Length:197
                                                                                                                                                                                                                                     
               SCOP domains d4hlcb_ B: automated matches                                                                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hlc B   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKNSDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEK 204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    || 157       167       177       187       197       
                                                                                                                                                                          146|                                                   
                                                                                                                                                                           153
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        KTHY_STAAR | Q6GJI9: 4gsy 4hld 4qg7 4qga 4qgf 4qgg 4qgh

(-) Related Entries Specified in the PDB File

4gsy
4gfd MOST POTENT GRAM NEGATIVE INHIBITOR OF THE COMPOUND SERIES
4hdc
4hej
4hld