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(-) Description

Title :  PYRROLOPYRIMIDINE INHIBITORS OF DNA GYRASE B AND TOPOISOMERASE IV, PART I: STRUCTURE GUIDED DISCOVERY AND OPTIMIZATION OF DUAL TARGETING AGENTS WITH POTENT, BROAD-SPECTRUM ENZYMATIC ACTIVITY
 
Authors :  D. C. Bensen, C. J. Creighton, L. W. Tari
Date :  06 Aug 12  (Deposition) - 13 Feb 13  (Release) - 27 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym./Biol. Unit :  A
Keywords :  Atp-Binding, Nucleotide-Binding, Topoisomerase, Atp-Binding Domain, Dna Gyrase Negatively Supercoils Closed Circular Double-Stranded Dna In An Atp-Dependent Manner And Also Catalyzes The Interconversion Of Other Topological Isomers Of Double-Stranded Dna Rings, Isomerase- Isomerase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. W. Tari, M. Trzoss, D. C. Bensen, X. Li, Z. Chen, T. Lam, J. Zhang, C. J. Creighton, M. L. Cunningham, B. Kwan, M. Stidham, K. J. Shaw, F. C. Lightstone, S. E. Wong, T. B. Nguyen, J. Nix, J. Finn
Pyrrolopyrimidine Inhibitors Of Dna Gyrase B (Gyrb) And Topoisomerase Iv (Pare). Part I: Structure Guided Discovery And Optimization Of Dual Targeting Agents With Potent, Broad-Spectrum Enzymatic Activity.
Bioorg. Med. Chem. Lett. V. 23 1529 2013
PubMed-ID: 23352267  |  Reference-DOI: 10.1016/J.BMCL.2012.11.032

(-) Compounds

Molecule 1 - DNA GYRASE SUBUNIT B
    ChainsA
    EC Number5.99.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    FragmentUNP RESIDUES 18-224
    GeneEF_0005, GYRB
    Organism ScientificENTEROCOCCUS FAECALIS
    Organism Taxid226185
    StrainATCC 700802 / V583

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1CJC1Ligand/Ion7-({4-[(3R)-3-AMINOPYRROLIDIN-1-YL]-5-CHLORO-6-ETHYL-7H-PYRROLO[2,3-D]PYRIMIDIN-2-YL}SULFANYL)PYRIDO[2,3-B]PYRAZIN-2(1H)-ONE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:48 , SER A:49 , GLU A:52 , ASP A:75 , ARG A:78 , GLY A:79 , ILE A:80 , PRO A:81 , GLY A:119 , SER A:122 , THR A:167 , VAL A:169 , HOH A:412 , HOH A:423 , HOH A:494 , HOH A:561 , HOH A:614BINDING SITE FOR RESIDUE CJC A 301
2AC2SOFTWAREALA A:53 , THR A:130 , ARG A:148 , ARG A:149 , ASN A:200 , ARG A:201 , LEU A:203 , HOH A:498 , HOH A:616BINDING SITE FOR RESIDUE GOL A 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4GGL)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 4GGL)

(-) 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    
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Chain A from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains d4ggla_ A: automated matches                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhh....hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee......eeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ggl A  18 GLEAVRKRPGMYIGSTSGEGLHHLVWEIVDNSIDEALAGFAKSIQVIIEPDDSITVIDDGRGIPVGIQAKTGRPAVETVFTVLHGVGSSVVNALSTSLDVRVYKDGKVYYQEYRRGAVVDDLKVIEETDRHGTTVHFIPDPEIFTETTVYDFDKLATRVRELAFLNRGLHISIEDRREGQEDKKEYHYEGLEH 227
                                    27        37        47        57        67        77        87        97   ||  124       134       144       154       164       174       184       194       204       214       224   
                                                                                                             101|                                                                                                            
                                                                                                              119                                                                                                            

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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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (12, 12)

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
        GYRB_ENTFA | Q839Z14gee 4gfn 4hxw 4k4o 4ksg 4ksh 4ktn

(-) Related Entries Specified in the PDB File

4gee 4gfn 4hxw 4hxz 4hy1 4hym 4hyp 4hz0 4hz5