5D7R

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.181 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery of Indazole Derivatives as a Novel Class of Bacterial Gyrase B Inhibitors.

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

(2015) Acs Med.Chem.Lett. 6: 1080-1085

  • DOI: 10.1021/acsmedchemlett.5b00266
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Antibacterials with a novel mechanism of action offer a great opportunity to combat widespread antimicrobial resistance. Bacterial DNA Gyrase is a clinically validated target. Through physiochemical property optimization of a pyrazolopyridone hit, a ...

    Antibacterials with a novel mechanism of action offer a great opportunity to combat widespread antimicrobial resistance. Bacterial DNA Gyrase is a clinically validated target. Through physiochemical property optimization of a pyrazolopyridone hit, a novel class of GyrB inhibitors were discovered. Guided by structure-based drug design, indazole derivatives with excellent enzymatic and antibacterial activity as well as great animal efficacy were discovered.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA gyrase subunit B
A, B
212Staphylococcus aureusMutation(s): 0 
Gene Names: gyrB
EC: 5.6.2.3
Find proteins for P0A0K8 (Staphylococcus aureus)
Go to UniProtKB:  P0A0K8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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Download CCD File 
A, B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
57Y
Query on 57Y

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Download CCD File 
A, B
3-hydroxy-5-[5-(6-hydroxy-7-propyl-2H-indazol-3-yl)-1,3-thiazol-2-yl]pyridine-2-carboxylic acid
C19 H16 N4 O4 S
YZWBQSFGTLQFTB-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
57YIC50: 13 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.181 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 143.192α = 90.00
b = 55.514β = 100.65
c = 51.114γ = 90.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
REFMACrefinement
MOLREPphasing
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-11-18
    Type: Initial release