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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, B Kwan, L. W. Tari
Date :  12 Nov 12  (Deposition) - 13 Feb 13  (Release) - 27 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
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 - TOPOISOMERASE IV, SUBUNIT B
    Chains: A, B
    EC Number: 5.99.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 1002-1383
    Gene: DNA TOPOISOMERASE IV SUBUNIT B PARE, FTL_1726
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. HOLARCTICA
    Organism Taxid: 376619
    Strain: LVS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
119X2Ligand/Ion6-({4-[(3R)-3-AMINOPYRROLIDIN-1-YL]-5-CHLORO-6-ETHYL-7H-PYRROLO[2,3-D]PYRIMIDIN-2-YL}SULFANYL)-1H-ISOINDOL-1-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
119X1Ligand/Ion6-({4-[(3R)-3-AMINOPYRROLIDIN-1-YL]-5-CHLORO-6-ETHYL-7H-PYRROLO[2,3-D]PYRIMIDIN-2-YL}SULFANYL)-1H-ISOINDOL-1-ONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
119X1Ligand/Ion6-({4-[(3R)-3-AMINOPYRROLIDIN-1-YL]-5-CHLORO-6-ETHYL-7H-PYRROLO[2,3-D]PYRIMIDIN-2-YL}SULFANYL)-1H-ISOINDOL-1-ONE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:38 , ASN A:41 , SER A:42 , GLU A:45 , ASP A:68 , ARG A:71 , GLY A:72 , MET A:73 , VAL A:115 , ARG A:131 , THR A:162 , ILE A:164 , HOH A:1512 , HOH A:1702 , HOH A:1783 , HOH A:1811 , HOH A:1845BINDING SITE FOR RESIDUE 19X A 1401
2AC2SOFTWAREILE B:38 , ASN B:41 , SER B:42 , GLU B:45 , ASP B:68 , ARG B:71 , GLY B:72 , MET B:73 , ILE B:89 , VAL B:115 , ARG B:131 , THR B:162 , HOH B:1507 , HOH B:1595BINDING SITE FOR RESIDUE 19X B 1401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HY1)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:227 -Ala A:228
2Leu A:231 -Pro A:232
3Leu B:231 -Pro B:232

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HY1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HY1)

(-) Exons   (0, 0)

(no "Exon" information available for 4HY1)

(-) 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:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains d4hy1a1 A:7-215 automated matches                                                                                                                                                                          d4hy1a2 A:216-377 automated matches                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee.....eeeee........ee....eehhhhhhhheeeee...........hhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeee.hhhh.....hhhhhhhhhhhhhhh....eeeeee....eeeee.......hhhhhhhh...eeeeeeeeeeee....eeeeeeee........eeeee..ee....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh.eeeeeeee.....ee.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hy1 A   7 KSIEVLTGLDPVKKRPGMYTNIENPNHLIQEIIDNSVDEVLAGFASKINITLYEDNSIEVADDGRGMPVDIHPEHKMSGIELIMTKLHSGGKFSNGGLHGVGVSVVNALSTRLEAEIKRDGNVYHIVFEDGFKTKDLEIIDNVGKKNTGTKIRFWPNKKYFDDIKVNFKALKNLLEAKAILCKALTIKYSNEIKKEKLTWHFETGLKGYLDHKLEAETLPAEPFIIDNFSNGDSYLDAVFCWCEDPSESIKNSYVNLIPTPQDGTHVTGLKNGIYDAIKAYIEKNSIKITANDSFAQLNYVISVKITNPQFAGQTKEKLSNKDVTNFVATAVKDLLTIWLNQNPDEARQIVENISKVAQK 377
                                    16        26        36        46        56        66        76        86        96    || 112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292     ||307       317       327       337       347       357       367       377
                                                                                                                        101|                                                                                                                                                                                           298|                                                                         
                                                                                                                         108                                                                                                                                                                                            304                                                                         


Chain B from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains d4hy1b1 B:8-215 automated matches                                                                                                                                                                   -------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .......hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh...eeeeee.....eeeee...............hhhhhhhhh..........hhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeee..........hhhhhhhhhhhhhhh....eeeeee....eeeee.......hhhhhhh..................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4hy1 B   8 SIEVLTGLDPVKKRPGMYTNIENPNHLIQEIIDNSVDEVLAGFASKINITLYEDNSIEVADDGRGMPVDIHPEHKMSGIELIMTKLHSGGKFSVGVSVVNALSTRLEAEIKRDGNVYHIVFEDGFKTKDLEIIDNVGKKNTGTKIRFWPNKKYFDDIKVNFKALKNLLEAKAILCKALTIKYSNEIKKEKLTWHFETGLKGYLDHKLAETLPAEPSESIKNSYVNLIP 271
                                    17        27        37        47        57        67        77        87        97  ||   119       129       139       149       159       169       179       189       199       209       219      |230   ||  263        
                                                                                                                      100|                                                                                                              226|   234|             
                                                                                                                       113                                                                                                               228    258
   Legend:   → Mismatch (orange background)
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  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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HY1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HY1)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4HY1)

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  4hy1
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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
        PARE_FRATH | A0A0J9WZF0: 4hxz 4hym 4kqv

(-) Related Entries Specified in the PDB File

4gee 4gfn 4ggl 4hxz 4hym 4hyp