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(-) Description

Title :  S. AUREUS GYRASE BOUND TO AN AMINOBENZIMIDAZOLE UREA INHIBITOR
 
Authors :  M. D. Jacobs
Date :  31 Mar 14  (Deposition) - 29 Oct 14  (Release) - 30 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Antibacterial, Gram-Positive, Gyrase, Topoisomerase, Staphylococcus Aureus, Isomerase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Grillot, A. L. Tiran, D. Shannon, E. Krueger, Y. Liao, H. O'Dowd, Q. Tang, S. Ronkin, T. Wang, N. Waal, P. Li, D. Lauffer, E. Sizensky, J. Tanoury, E. Perola, T. H. Grossman, T. Doyle, B. Hanzelka, S. Jones, V. Dixit, N. Ewing, S. Liao, B. Boucher, M. Jacobs, Y. Bennani, P. S. Charifson
Second-Generation Antibacterial Benzimidazole Ureas: Discovery Of A Preclinical Candidate With Reduced Metabolic Liability.
J. Med. Chem. V. 57 8792 2014
PubMed-ID: 25317480  |  Reference-DOI: 10.1021/JM500563G

(-) Compounds

Molecule 1 - DNA GYRASE 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
    Gene: GYRB, SAR0005
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 703339
    Other Details: ATPASE DOMAIN WITH LOOP DELETION
    Strain: 04-02981

 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
18832Ligand/Ion1-ETHYL-3-[5-(5-FLUOROPYRIDIN-3-YL)-7-(PYRIMIDIN-2-YL)-1H-BENZIMIDAZOL-2-YL]UREA
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
18831Ligand/Ion1-ETHYL-3-[5-(5-FLUOROPYRIDIN-3-YL)-7-(PYRIMIDIN-2-YL)-1H-BENZIMIDAZOL-2-YL]UREA
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
18831Ligand/Ion1-ETHYL-3-[5-(5-FLUOROPYRIDIN-3-YL)-7-(PYRIMIDIN-2-YL)-1H-BENZIMIDAZOL-2-YL]UREA

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:54 , SER A:55 , GLU A:58 , VAL A:79 , ASP A:81 , ARG A:84 , GLY A:85 , ILE A:86 , PRO A:87 , ILE A:102 , ARG A:144 , THR A:173 , HOH A:442 , HOH A:471 , THR B:185 , GLU B:186binding site for residue 883 A 301
2AC2SOFTWAREILE B:51 , ASN B:54 , SER B:55 , GLU B:58 , VAL B:79 , ASP B:81 , ARG B:84 , GLY B:85 , ILE B:86 , PRO B:87 , ARG B:144 , HOH B:422 , HOH B:442 , HOH B:478binding site for residue 883 B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P8O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P8O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P8O)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P8O)

(-) Exons   (0, 0)

(no "Exon" information available for 4P8O)

(-) 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:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeeeehhheeeeee...............hhhhhhhh.hhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p8o A  24 GLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    33        43        53        63        73        83        93       103||     136       146       156       166       176       186       196       206       216       226    
                                                                                                          104|                                                                                                      
                                                                                                           128                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:184
                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh....eeeeeee...eeeeee...............hhhhhhhh.hhhhhheeeeeeeeee..eeeeeeee..ee....eeeee....eeeeeeee...........hhhhhhhhhhhhhhhh...eeeeee.....eeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p8o B  24 GLEAVRKRPGMYIGSTSERGLHHLVWEIVDNSIDEALAGYANQIEVVIEKDNWIKVTDNGRGIPVDIQEKMGRPAVEVILTSSVVNALSQDLEVYVHRNETIYHQAYKKGVPQFDLKEVGTTDKTGTVIRFKADGEIFTETTVYNYETLQQRIRELAFLNKGIQITLRDERDEENVREDSYHYE 230
                                    33        43        53        63        73        83        93       103||     136       146       156       166       176       186       196       206       216       226    
                                                                                                          104|                                                                                                      
                                                                                                           128
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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  (0, 0)

(no "SCOP Domain" information available for 4P8O)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P8O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P8O)

(-) Gene Ontology  (12, 12)

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