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(-) Description

Title :  S.AUREUS TMK IN COMPLEX WITH THE POTENT INHIBITOR COMPOUND 38, 2-(3-CHLOROPHENOXY)-3-METHOXY-4-{(1R)-1-[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]PROPYL}BENZOIC ACID
 
Authors :  N. B. Olivier
Date :  22 May 14  (Deposition) - 11 Jun 14  (Release) - 02 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Thymidine Monphosphate, Soluble, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. P. Kawatkar, T. A. Keating, N. B. Olivier, J. N. Breen, O. M. Green, S. Y. Guler, M. F. Hentemann, J. T. Loch, A. R. Mckenzie, J. V. Newman, L. G. Otterson, G. Martinez-Botella
Antibacterial Inhibitors Of Gram-Positive Thymidylate Kinase: Structure-Activity Relationships And Chiral Preference Of A New Hydrophobic Binding Region.
J. Med. Chem. V. 57 4584 2014
PubMed-ID: 24828090  |  Reference-DOI: 10.1021/JM500463C

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: TMK
    Gene: SAR0483, TMK
    Mutation: YES
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 282458
    Strain: N314
    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
132B2Ligand/Ion2-(3-CHLOROPHENOXY)-3-METHOXY-4-{(1R)-1-[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL]PROPYL}BENZOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:37 , ARG A:48 , VAL A:51 , 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:413 , HOH A:414 , HOH A:502 , HOH A:503 , HIS B:172 , SER B:175BINDING SITE FOR RESIDUE 32B A 301
2AC2SOFTWAREGLU B:37 , ARG B:48 , VAL B:51 , PHE B:66 , SER B:69 , ARG B:70 , ARG B:92 , SER B:97 , TYR B:100 , GLN B:101 , HOH B:524 , HOH B:525 , HOH B:526BINDING SITE FOR RESIDUE 32B B 301

(-) SS Bonds  (0, 0)

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

(-) 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 4QGF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4QGF)

(-) 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:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- 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
                 4qgf A   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141  ||   159       169       179       189       199      
                                                                                                                                                                        144|                                                    
                                                                                                                                                                         153                                                    


Chain B from PDB  Type:PROTEIN  Length:194
                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qgf B   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141||     161       171       181       191       201    
                                                                                                                                                                      142|                                                    
                                                                                                                                                                       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  (0, 0)

(no "SCOP Domain" information available for 4QGF)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 4hlc 4hld 4qg7 4qga 4qgg 4qgh

(-) Related Entries Specified in the PDB File

4qg7 4qgf 4qgg 4qgh