Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.53 kDa 
• Atom Count: 1,682 
• Modelled Residue Count: 196 
• Deposited Residue Count: 220 
• Unique protein chains: 1

 6KZZ

Crystal structure of E.coli DNA gyrase B in complex with 2-oxo-1,2-dihydroquinoline derivative

• PDB DOI:  https://doi.org/10.2210/pdb6KZZ/pdb

• Classification: ISOMERASE
• Organism(s): Escherichia coli
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2019-09-25 Released: 2020-05-06 
• Deposition Author(s): Mima, M., Takeuchi, T., Ushiyama, F.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.238 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 

Literature

Lead Identification of 8-(Methylamino)-2-oxo-1,2-dihydroquinoline Derivatives as DNA Gyrase Inhibitors: Hit-to-Lead Generation Involving Thermodynamic Evaluation.

Ushiyama, F., Amada, H., Takeuchi, T., Tanaka-Yamamoto, N., Kanazawa, H., Nakano, K., Mima, M., Masuko, A., Takata, I., Hitaka, K., Iwamoto, K., Sugiyama, H., Ohtake, N.

(2020) ACS Omega 5: 10145-10159

• PubMed: 32391502 
• DOI: https://doi.org/10.1021/acsomega.0c00865
• Primary Citation of Related Structures:  
  6KZV, 6KZX, 6KZZ, 6L01


• PubMed Abstract: 
  

DNA gyrase and topoisomerase IV are well-validated pharmacological targets, and quinolone antibacterial drugs are marketed as their representative inhibitors. However, in recent years, resistance to these existing drugs has become a problem, and new chemical classes of antibiotics that can combat resistant strains of bacteria are strongly needed. In this study, we applied our hit-to-lead (H2L) chemistry for the identification of a new chemical class of GyrB/ParE inhibitors by efficient use of thermodynamic parameters. Investigation of the core fragments obtained by fragmentation of high-throughput screening hit compounds and subsequent expansion of the hit fragment was performed using isothermal titration calorimetry (ITC). The 8-(methylamino)-2-oxo-1,2-dihydroquinoline derivative 13e showed potent activity against Escherichia coli DNA gyrase with an IC ₅₀ value of 0.0017 μM. In this study, we demonstrated the use of ITC for primary fragment screening, followed by structural optimization to obtain lead compounds, which advanced into further optimization for creating novel antibacterial agents.

---

Organizational Affiliation: 

Chemistry Laboratories, Taisho Pharmaceutical Company Ltd., 1-403, Yoshino-Cho, Kita-Ku, Saitama, Saitama 331-9530, Japan.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA gyrase subunit B	A	220	Escherichia coli	Mutation(s): 0  Gene Names: gyrB, C9Z04_12785 EC: 5.6.2.2
UniProt
Find proteins for P0AES6 (Escherichia coli (strain K12)) Explore P0AES6  Go to UniProtKB:  P0AES6

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E0R (Subject of Investigation/LOI)	B [auth A]	4-[[8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]benzoic acid C18 H15 N3 O4 VUXYPRAXFABKBH-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E0R	Binding MOAD:  6KZZ	IC50: 1.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.238 
• R-Value Work: 0.190 
• R-Value Observed: 0.193 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.303	α = 90
b = 67.08	β = 90
c = 68.285	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
CrystalClear	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): Mima, M., Takeuchi, T., Ushiyama, F.

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2020-05-27
  Changes: Database references