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(-) Description

Title :  DISCOVERY OF SELECTIVE AND POTENT INHIBITORS OF GRAM-POSITIVE BACTERIAL THYMIDYLATE KINASE (TMK: COMPOUND 41)
 
Authors :  N. B. Olivier
Date :  02 Oct 12  (Deposition) - 24 Oct 12  (Release) - 02 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kinase, Tmp, Active Site, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Martinez-Botella, J. N. Breen, J. E. Duffy, J. Dumas, B. Geng, I. K. Gowers, O. M. Green, S. Guler, M. F. Hentemann, F. A. Hernandez-Juan, D. Joseph-Mccarthy, S. Kawatkar, N. A. Larsen, O. Lazari, J. T. Loch, J. A. Macritchie, A. R. Mckenzie, J. V. Newman, N. B. Olivier, L. G. Otterson, A. P. Owens, J. Read, D. W. Sheppard, T. A. Keating
Discovery Of Selective And Potent Inhibitors Of Gram-Positive Bacterial Thymidylate Kinase (Tmk).
J. Med. Chem. V. 55 10010 2012
PubMed-ID: 23043329  |  Reference-DOI: 10.1021/JM3011806

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30A
    Expression System Strain: BL21-CODON +
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: SA0440, TMK
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 158879
    Strain: MW2
    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
113Y2Ligand/Ion2-(3-CHLOROPHENOXY)-4-{(1R)-3-METHYL-1-[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]BUTYL}BENZOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:37 , ARG A:48 , PHE A:66 , SER A:69 , ARG A:70 , ARG A:92 , SER A:97 , TYR A:100 , GLN A:101 , HOH A:411 , HOH A:443 , HOH A:452 , HIS B:172 , SER B:175BINDING SITE FOR RESIDUE 13Y A 301
2AC2SOFTWAREGLU B:11 , GLU B:37 , ARG B:48 , LEU B:52 , 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:463BINDING SITE FOR RESIDUE 13Y B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:37 -Pro A:38
2Ile A:142 -Ile A:143
3Glu B:37 -Pro B:38

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HDC)

(-) 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 d4hdca_ A: automated matches                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhh...hhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hdc A   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141 ||    160       170       180       190       200     
                                                                                                                                                                       143|                                                    
                                                                                                                                                                        153                                                    


Chain B from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains d4hdcb_ 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.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hdc B   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKNSDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141    || 157       167       177       187       197        
                                                                                                                                                                          146|                                                    
                                                                                                                                                                           153
   Legend:   → Mismatch (orange background)
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  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/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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_STAAN | P65249: 4gfd 4gsy 4hej

(-) Related Entries Specified in the PDB File

4gfd MOST POTENT COMPOUND OF THE PIPERIDINE SERIES.
4gsy
4hej