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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 :  14 Nov 12  (Deposition) - 13 Feb 13  (Release) - 27 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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 - DNA TOPOISOMERASE 4 SUBUNIT B
    Chains: A, B
    EC Number: 5.99.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Fragment: UNP RESIDUES 12-216
    Gene: B3030, DNA TOPOISOMERASE IV SUBUNIT B PARE, JW2998, NFXD, PARE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: TOPOISOMERASE IV SUBUNIT B

 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  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
11AV2Ligand/Ion7-(1H-IMIDAZOL-1-YL)-2-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-D]PYRIMIDIN-5-AMINE
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11AV1Ligand/Ion7-(1H-IMIDAZOL-1-YL)-2-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-D]PYRIMIDIN-5-AMINE
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11AV1Ligand/Ion7-(1H-IMIDAZOL-1-YL)-2-(PYRIDIN-3-YL)[1,3]THIAZOLO[5,4-D]PYRIMIDIN-5-AMINE
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:42 , SER A:43 , GLU A:46 , ASP A:69 , ARG A:72 , GLY A:73 , PRO A:75 , ILE A:90 , HOH A:414 , HOH A:430 , HOH A:446BINDING SITE FOR RESIDUE 1AV A 301
2AC2SOFTWAREHIS A:186BINDING SITE FOR RESIDUE MG A 302
3AC3SOFTWAREASN B:42 , SER B:43 , GLU B:46 , ASP B:69 , ARG B:72 , GLY B:73 , MET B:74 , ILE B:90 , HOH B:404 , HOH B:417BINDING SITE FOR RESIDUE 1AV B 301
4AC4SOFTWAREHIS B:186 , HOH B:498BINDING SITE FOR RESIDUE MG B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4HZ0)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:108 -Gly A:109
2Ser B:108 -Gly B:109

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4HZ0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4HZ0)

(-) Exons   (0, 0)

(no "Exon" information available for 4HZ0)

(-) 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:201
                                                                                                                                                                                                                                         
               SCOP domains d4hz0a_ A: automated matches                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee.....eeeee........ee....eehhhhhhhh.....eee....eee....hhhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeee.hhhh.....hhhhhhhhhhhhhhhh...eeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hz0 A  14 TGLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLVGISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCYQ 216
                                    23        33        43        53        63        73        83        93       103       115       125       135       145       155       165       175       185       195       205       215 
                                                                                                                           111|                                                                                                      
                                                                                                                            114                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:201
                                                                                                                                                                                                                                         
               SCOP domains d4hz0b_ B: automated matches                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....eeeeee.....eeeee...............hhhhhhhhh......ee....ee.....hhhhhhhheeeeeeeeee..eeeeeeee..eeeeeeeeeee......eeeeeeee.hhhh.....hhhhhhhhhhhhhhhh...eeeeee....eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hz0 B  14 TGLEPVRRRPGMYTDTTRPNHLGQEVIDNSVDEALAGHAKRVDVILHADQSLEVIDDGRGMPVDIHPEEGVPAVELILCRLHAGGKFSNKNYQFSGGLVGISVVNALSKRVEVNVRRDGQVYNIAFENGEKVQDLQVVGTCGKRNTGTSVHFWPDETFFDSPRFSVSRLTHVLKAKAVLCPGVEITFKDEINNTEQRWCYQ 216
                                    23        33        43        53        63        73        83        93       103       115       125       135       145       155       165       175       185       195       205       215 
                                                                                                                           111|                                                                                                      
                                                                                                                            114
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4HZ0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4HZ0)

(-) Gene Ontology  (19, 19)

Asymmetric Unit(hide GO term definitions)

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  4hz0
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  PARE_ECOLI | P20083
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  5.99.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        PARE_ECOLI | P20083: 1s14 1s16 3fv5

(-) Related Entries Specified in the PDB File

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