7C7N

Crystal structure of E.coli DNA gyrase B in complex with 6-fluoro-8-(methylamino)-2-oxo-1,2-dihydroquinoline derivative

• PDB DOI: https://doi.org/10.2210/pdb7C7N/pdb

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


• Deposited: 2020-05-26 Released: 2020-10-14 
• Deposition Author(s): Mima, M., Ushiyama, F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.276 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 

Literature

Lead optimization of 8-(methylamino)-2-oxo-1,2-dihydroquinolines as bacterial type II topoisomerase inhibitors.

Ushiyama, F., Amada, H., Mihara, Y., Takeuchi, T., Tanaka-Yamamoto, N., Mima, M., Kamitani, M., Wada, R., Tamura, Y., Endo, M., Masuko, A., Takata, I., Hitaka, K., Sugiyama, H., Ohtake, N.

(2020) Bioorg Med Chem 28: 115776-115776

• PubMed: 33032189 
• DOI: https://doi.org/10.1016/j.bmc.2020.115776
• Primary Citation of Related Structures:  
  7C7N, 7C7O


• PubMed Abstract: 
  

  The global increase in multidrug-resistant pathogens has caused severe problems in the treatment of infections. To overcome these difficulties, the advent of a new chemical class of antibacterial drug is eagerly desired. We aimed at creating novel antibacterial agents against bacterial type II topoisomerases, which are well-validated targets. TP0480066 (compound 32) has been identified by using structure-based optimization originated from lead compound 1, which was obtained as a result of our previous lead identification studies. The MIC ₉₀ values of TP0480066 against methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant Enterococci (VRE), and genotype penicillin-resistant Streptococcus pneumoniae (gPRSP) were 0.25, 0.015, and 0.06 μg/mL, respectively. Hence, TP0480066 can be regarded as a promising antibacterial drug candidate of this chemical class.

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Organizational Affiliation: 

Taisho Pharmaceutical Co., Ltd, 1-403 Yoshino-Cho, Kita-Ku, Saitama 331-9530, Japan. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 24.55 kDa 
• Atom Count: 1,600 
• Modelled Residue Count: 198 
• Deposited Residue Count: 220 
• Unique protein chains: 1

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, NCTC10766_01911, NCTC9007_05029 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
FKR (Subject of Investigation/LOI)	B [auth A]	4-[[6-fluoranyl-8-(methylamino)-2-oxidanylidene-1~{H}-quinolin-3-yl]carbonylamino]benzoic acid C18 H14 F N3 O4 DFAPUBLMKMWKJW-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
FKR	Binding MOAD:  7C7N	IC50: 0.36 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.276 
• R-Value Work: 0.206 
• R-Value Observed: 0.209 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.333	α = 90
b = 67.052	β = 90
c = 68.213	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: 2020-10-14 
Deposition Author(s): Mima, M., Ushiyama, F.

Revision History  

• Version 1.0: 2020-10-14
  Type: Initial release
  
• Version 1.1: 2020-10-21
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description