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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 :  13 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 Taxid: 562
    Gene: FTL_1726
    Organism Scientific: FRANCISELLA TULARENSIS SUBSP. HOLARCTICA LVS
    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, 1)

Asymmetric Unit (1, 1)
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
Biological Unit 1 (1, 1)
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
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CJC-1Ligand/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

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:38 , ASN A:41 , SER A:42 , GLU A:45 , ASP A:68 , GLY A:72 , MET A:73 , ILE A:89 , VAL A:115 , ARG A:131 , THR A:162 , ILE A:164 , HOH A:526 , HOH A:530 , HOH A:675 , HOH A:791 , HOH A:842BINDING SITE FOR RESIDUE CJC A 401

(-) SS Bonds  (0, 0)

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

(-) 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 4HYM)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HYM)

(-) 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:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4hyma1 A:7-215 automated matches                                                                                                                                                                          d4hyma2 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.............................................................................................................................................................................................................................................................................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hym A   7 KSIEVLTGLDPVKKRPGMYTNIENPNHLIQEIIDNSVDEVLAGFASKINITLYEDNSIEVADDGRGMPVDIHPEHKMSGIELIMTKLHSGGKFSNGGLHGVGVSVVNALSTRLEAEIKRDGNVYHIVFEDGFKTKDLEIIDNVGKKNTGTKIRFWPNKKYFDDIKVNFKALKNLLEAKAILCKALTIKYSNEIKKEKLTWHFETGLKGYLDHKLEAETLPAEPFIIDNFSNGDSYLDAVFCWCEDPSESIKNSYVNLIPTPQDGTHVTGLKNGIYDAIKAYIEKNSNIKITANDSFAQLNYVISVKITNPQFAGQTKEKLSNKDVTNFVATAVKDLLTIWLNQNPDEARQIVENISKVAQK 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     ||306       316       326       336       346       356       366       376 
                                                                                                                        101|                                                                                                                                                                                           298|                                                                          
                                                                                                                         108                                                                                                                                                                                            303                                                                          


Chain B from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains d4hymb1 B:8-215 automated matches                                                                                                                                                                   ------------------------------ SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhh...ee.....hhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeee.hhhh.....hhhhhhhhhhhhhhh....eeeeee....eeeee.......hhhhhhhh.................. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hym B   8 SIEVLTGLDPVKKRPGMYTNIENPNHLIQEIIDNSVDEVLAGFASKINITLYEDNSIEVADDGRGMPVDIHPEHKMSGIELIMTKLHSGGKFSVGVSVVNALSTRLEAEIKRDGNVYHIVFEDGFKTKDLEIIDNVGKKNTGTKIRFWPNKKYFDDIKVNFKALKNLLEAKAILCKALTIKYSNEIKKEKLTWHFETGLKGYLDHKLEAETLPASIKNSYNLIPTP 273
                                    17        27        37        47        57        67        77        87        97  ||   119       129       139       149       159       169       179       189       199       209       219       229   ||  266|     
                                                                                                                      100|                                                                                                                     233|  266|     
                                                                                                                       113                                                                                                                      261   268
   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 4HYM)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  5.99.1.3
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 Related Entries

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

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        PARE_FRATH | A0A0J9WZF0: 4hxz 4hy1 4kqv

(-) Related Entries Specified in the PDB File

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