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(-) Description

Title :  TMK FROM S.AUREUS IN COMPLEX WITH THE PIPERIDINYL THYMINE CLASS INHIBITOR WITH A C5 ETHYL-AMINE
 
Authors :  N. B. Olivier
Date :  28 Jan 15  (Deposition) - 11 Feb 15  (Release) - 11 Feb 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tmk, Kinase, Antibacterial, Piperidine, Thymidine, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Y. Guler, G. Martinez-Botella, J. Breen, S. Kawatkar, J. Loch, N. B. Olivier, H. Wang, T. Keating, L. Otterson
A Highly Potent Antibacterial Inhibitor Of Gram-Positive Bacterial Thymidylate Kinase (Tmk): Sar Of Piperidinyl Thymines At Position C5 And L1
Bioorg Med Chem Lett 2015
PubMed: search

(-) Compounds

Molecule 1 - THYMIDYLATE KINASE
    Chains: A, B
    EC Number: 2.7.4.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Taxid: 511693
    Gene: TMK, SAHV_0479
    Organism Scientific: STAPHYLOCOCCUS AUREUS (STRAIN MU3 / ATCC 700698)
    Organism Taxid: 418127
    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
143N2Ligand/Ion2-(3-CHLOROPHENOXY)-6-(ETHYLAMINO)-4-[(R)-[(3S)-3-(5-METHYL-2,4-DIOXO-3,4-DIHYDROPYRIMIDIN-1(2H)-YL)PIPERIDIN-1-YL](PHENYL)METHYL]BENZOIC ACID

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:37 , ARG A:48 , GLU A:62 , PHE A:66 , SER A:69 , ARG A:70 , ARG A:92 , SER A:97 , TYR A:100 , GLN A:101 , HOH A:476 , HOH A:537 , HOH A:566 , HIS B:172binding site for residue 43N A 301
2AC2SOFTWAREGLU 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:406 , HOH B:510 , HOH B:543binding site for residue 43N B 301

(-) SS Bonds  (0, 0)

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

(-) 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 4XWA)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XWA)

(-) 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:200
                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xwa A   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKNSRLDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141     ||155       165       175       185       195       205
                                                                                                                                                                           147|                                                     
                                                                                                                                                                            152                                                     


Chain B from PDB  Type:PROTEIN  Length:198
                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......hhhhhhhhhhhhhh.....eeeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xwa B   2 SAFITFEGPEGSGKTTVINEVYHRLVKDYDVIMTREPGGVPTGEEIRKIVLEGNDMDIRTEAMLFAASRREHLVLKVIPALKEGKVVLCDRYIDSSLAYQGYARGIGVEEVRALNEFAINGLYPDLTIYLNVSAEVGRERIIKNLDQEDLKFHEKVIEGYQEIIHNESQRFKSVNADQPLENVVEDTYQTIIKYLEKI 205
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141   ||  157       167       177       187       197        
                                                                                                                                                                         145|                                                     
                                                                                                                                                                          152
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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 4XWA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)

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