5D6P

Crystal structure of the ATP binding domain of S. aureus GyrB complexed with a ligand


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 

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Ligand Structure Quality Assessment 


This is version 1.0 of the entry. See complete history


Literature

Discovery of Azaindole Ureas as a Novel Class of Bacterial Gyrase B Inhibitors.

Zhang, J.Yang, Q.Cross, J.B.Romero, J.A.Poutsiaka, K.M.Epie, F.Bevan, D.Wang, B.Zhang, Y.Chavan, A.Zhang, X.Moy, T.Daniel, A.Nguyen, K.Chamberlain, B.Carter, N.Shotwell, J.Silverman, J.Metcalf, C.A.Ryan, D.Lippa, B.Dolle, R.E.

(2015) J Med Chem 58: 8503-8512

  • DOI: 10.1021/acs.jmedchem.5b00961
  • Primary Citation of Related Structures:  
    5D6P, 5D6Q, 5D7C

  • PubMed Abstract: 
  • The emergence and spread of multidrug resistant bacteria are widely believed to endanger human health. New drug targets and lead compounds exempt from cross-resistance with existing drugs are urgently needed. We report on the discovery of azaindole ureas as a novel class of bacterial gyrase B inhibitors and detail the story of their evolution from a de novo design hit based on structure-based drug design ...

    The emergence and spread of multidrug resistant bacteria are widely believed to endanger human health. New drug targets and lead compounds exempt from cross-resistance with existing drugs are urgently needed. We report on the discovery of azaindole ureas as a novel class of bacterial gyrase B inhibitors and detail the story of their evolution from a de novo design hit based on structure-based drug design. These inhibitors show potent minimum inhibitory concentrations against fluoroquinolone resistant MRSA and other Gram-positive bacteria.


    Organizational Affiliation

    Cubist Pharmaceuticals Inc. , Lexington, Massachusetts 02421, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
DNA gyrase subunit BA, B212Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB
EC: 5.99.1.3 (PDB Primary Data), 5.6.2.2 (UniProt)
UniProt
Find proteins for P0A0K8 (Staphylococcus aureus)
Explore P0A0K8 
Go to UniProtKB:  P0A0K8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A0K8
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
57U
Query on 57U

Download Ideal Coordinates CCD File 
C [auth A],
F [auth B]
1-ethyl-3-[4-(hydroxymethyl)-5-(1H-pyrrol-2-yl)-1,3-thiazol-2-yl]urea
C11 H14 N4 O2 S
YLSYQKDIZQYYGN-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download Ideal Coordinates CCD File 
D [auth A],
G [auth B],
H [auth B]
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
E [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
57U BindingDB:  5D6P IC50: 2500 (nM) from 1 assay(s)
Binding MOAD:  5D6P IC50: 2500 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.208 
  • R-Value Observed: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 144.539α = 90
b = 55.556β = 99.73
c = 51.113γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2015-11-25
    Type: Initial release