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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, M. Trzoss, L. W. Tari
Date :  12 Nov 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, 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
    Chains: A
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: EF_0005, GYRB
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 226185
    Strain: ATCC 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
11A01Ligand/Ion(3R)-1-[5-CHLORO-6-ETHYL-2-(PYRIDO[2,3-B]PYRAZIN-7-YLSULFANYL)-7H-PYRROLO[2,3-D]PYRIMIDIN-4-YL]PYRROLIDIN-3-AMINE
2TBU1Ligand/IonTERTIARY-BUTYL ALCOHOL

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:55 , SER A:56 , GLU A:59 , ASP A:82 , ARG A:85 , GLY A:86 , ILE A:87 , PRO A:88 , SER A:129 , THR A:174 , HOH A:414 , HOH A:484BINDING SITE FOR RESIDUE 1A0 A 301
2AC2SOFTWAREALA A:60 , THR A:137 , ARG A:155 , ARG A:156 , ASN A:207 , ARG A:208 , HOH A:586BINDING SITE FOR RESIDUE TBU A 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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 Sequence-Structure Mapping

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

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(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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  UniProt sequence: complete  aligned part    
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:191
                                                                                                                                                                                                                               
               SCOP domains d4hxwa_ A: automated matches                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhh..hhhhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee......eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hxw A  25 GLEAVRKRPGMYIGSTSGEGLHHLVWEIVDNSIDEALAGFAKSIQVIIEPDDSITVIDDGRGIPVGIQAKTGRPAVETVFTVLVGSSVVNALSTSLDVRVYKDGKVYYQEYRRGAVVDDLKVIEETDRHGTTVHFIPDPEIFTETTVYDFDKLATRVRELAFLNRGLHISIEDRREGQEDKKEYHYEGLEH 234
                                    34        44        54        64        74        84        94       104  ||   133       143       153       163       173       183       193       203       213       223       233 
                                                                                                            107|                                                                                                           
                                                                                                             127
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 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)

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  4hxw
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  GYRB_ENTFA | Q839Z1
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  5.99.1.3
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 Related Entries

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

UniProtKB/Swiss-Prot
        GYRB_ENTFA | Q839Z1: 4gee 4gfn 4ggl 4k4o 4ksg 4ksh 4ktn

(-) Related Entries Specified in the PDB File

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