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(-) Description

Title :  NOVEL N-PHENYL-PHENOXYACETAMIDE DERIVATIVES AS POTENTIAL ETHR INHIBITORS AND ETHIONAMIDE BOOSTERS. DISCOVERY AND OPTIMIZATION USING HIGH-THROUGHPUT SYNTHESIS.
 
Authors :  M. Flipo, N. Willand, N. Lecat-Guillet, C. Hounsou, M. Desroses, F. Ler Z. Lens, V. Villeret, A. Wohlkonig, R. Wintjens, T. Christophe, H. K. J C. Locht, P. Brodin, A. R. Baulard, B. Deprez
Date :  24 Feb 12  (Deposition) - 27 Mar 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Tetr-Family, Transcritptional Regulatory Repressor, Inhibitor, Dna Binding Protein, Transcription Repressor-Inhibitor Complex, Transcription-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Flipo, N. Willand, N. Lecat-Guillet, C. Hounsou, M. Desroses, F. Leroux, Z. Lens, V. Villeret, A. Wohlkonig, R. Wintjens, T. Christophe, H. Kyoung Jeon, C. Locht, P. Brodin, A. R. Baulard, B. Deprez
Discovery Of Novel N-Phenylphenoxyacetamide Derivatives As Ethr Inhibitors And Ethionamide Boosters By Combining High-Throughput Screening And Synthesis.
J. Med. Chem. V. 55 6391 2012
PubMed-ID: 22738293  |  Reference-DOI: 10.1021/JM300377G

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR ETHR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: ETAR, ETHR, MT3970, RV3855
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 1773
    Strain: H37RV

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
10MN1Ligand/IonN-[4-(1,3-BENZOTHIAZOL-2-YL)PHENYL]-2-(3-METHOXYPHENOXY)ACETAMIDE
2GOL3Ligand/IonGLYCEROL
3NH41Ligand/IonAMMONIUM ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
10MN2Ligand/IonN-[4-(1,3-BENZOTHIAZOL-2-YL)PHENYL]-2-(3-METHOXYPHENOXY)ACETAMIDE
2GOL6Ligand/IonGLYCEROL
3NH42Ligand/IonAMMONIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:87 , MET A:102 , GLY A:106 , ILE A:107 , PHE A:110 , TRP A:138 , MET A:142 , TYR A:148 , THR A:149 , VAL A:152 , ASN A:176 , ASN A:179 , GLU A:180 , LEU A:183 , PHE A:184 , TRP A:207BINDING SITE FOR RESIDUE 0MN A 301
2AC2SOFTWAREGLY A:115BINDING SITE FOR RESIDUE NH4 A 302
3AC3SOFTWAREASP A:154 , ARG A:157 , THR A:165 , LEU A:166 , PRO A:167 , ALA A:168 , HOH A:431 , HOH A:447BINDING SITE FOR RESIDUE GOL A 303
4AC4SOFTWARESER A:46 , VAL A:47 , ASP A:48 , ARG A:58BINDING SITE FOR RESIDUE GOL A 304
5AC5SOFTWARETYR A:62 , PRO A:66 , ASN A:93 , THR A:97BINDING SITE FOR RESIDUE GOL A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DW6)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:191 -Pro A:192

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DW6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DW6)

(-) Exons   (0, 0)

(no "Exon" information available for 4DW6)

(-) 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:188
 aligned with ETHR_MYCTO | P9WMC0 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:191
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213 
           ETHR_MYCTO    24 DRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFPSKEAVLLTLLDRVVNQADMALQTLAENPADTDRENMWRTGINVFFETFGSHKAVTRAGQAARATSVEVAELWSTFMQKWIAYTAAVIDAERDRGAAPRTLPAHELATALNLMNERTLFASFAGEQPSVPEARVLDTLVHIWVTSIYGE 214
               SCOP domains d4dw6a1 A:24-93 automated matches                                     ---d4dw6a2 A:97-214 automated matches                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.---.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dw6 A  24 DRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFPSKEAVLLTLLDRVVNQADMALQTLAEN---TDRENMWRTGINVFFETFGSHKAVTRAGQAARATSVEVAELWSTFMQKWIAYTAAVIDAERDRGAAPRTLPAHELATALNLMNERTLFASFAGEQPSVPEARVLDTLVHIWVTSIYGE 214
                                    33        43        53        63        73        83        93   |   103       113       123       133       143       153       163       173       183       193       203       213 
                                                                                                93  97                                                                                                                     


Chain A from PDB  Type:PROTEIN  Length:188
 aligned with ETHR_MYCTU | P9WMC1 from UniProtKB/Swiss-Prot  Length:216

    Alignment length:191
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213 
           ETHR_MYCTU    24 DRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFPSKEAVLLTLLDRVVNQADMALQTLAENPADTDRENMWRTGINVFFETFGSHKAVTRAGQAARATSVEVAELWSTFMQKWIAYTAAVIDAERDRGAAPRTLPAHELATALNLMNERTLFASFAGEQPSVPEARVLDTLVHIWVTSIYGE 214
               SCOP domains d4dw6a1 A:24-93 automated matches                                     ---d4dw6a2 A:97-214 automated matches                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.---.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dw6 A  24 DRELAILATAENLLEDRPLADISVDDLAKGAGISRPTFYFYFPSKEAVLLTLLDRVVNQADMALQTLAEN---TDRENMWRTGINVFFETFGSHKAVTRAGQAARATSVEVAELWSTFMQKWIAYTAAVIDAERDRGAAPRTLPAHELATALNLMNERTLFASFAGEQPSVPEARVLDTLVHIWVTSIYGE 214
                                    33        43        53        63        73        83        93   |   103       113       123       133       143       153       163       173       183       193       203       213 
                                                                                                93  97
   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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DW6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DW6)

(-) Gene Ontology  (7, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (ETHR_MYCTU | P9WMC1)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0046677    response to antibiotic    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Chain A   (ETHR_MYCTO | P9WMC0)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ETHR_MYCTO | P9WMC0: 1t56 1u9n 1u9o 3g1l 3g1m 3g1o 3o8g 3o8h 3q0u 3q0v 3q0w 3q3s 3qpl 3sdg 3sfi 3tp0 3tp3 4m3b 4m3d 4m3e 4m3f 4m3g 5ezg 5ezh 5f04 5f08 5f0c 5f0f 5f0h 5f1j 5f27 5j3l
        ETHR_MYCTU | P9WMC1: 1t56 1u9n 1u9o 3g1l 3g1m 3g1o 3o8g 3o8h 3q0u 3q0v 3q0w 3q3s 3qpl 3sdg 3sfi 3tp0 3tp3 4m3b 4m3d 4m3e 4m3f 4m3g 5eyr 5ezg 5ezh 5f04 5f08 5f0c 5f0f 5f0h 5f1j 5f27 5j1r 5j1u 5j1y 5j3l 5mwo 5mxk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4DW6)