6HVI | pdb_00006hvi

Human PFKFB3 in complex with a N-Aryl 6-Aminoquinoxaline inhibitor 2

• PDB DOI: https://doi.org/10.2210/pdb6HVI/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-10-11 Released: 2018-11-14 
• Deposition Author(s): Banaszak, K., Sowinska, M., Gondela, A., Fabritius, C.H., Nowak, M.
• Funding Organization(s): European Regional Development Fund

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free: 
  0.208 (Depositor), 0.215 (DCC) 
• R-Value Work: 
  0.186 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.187 (Depositor) 

Literature

Discovery and Structure-Activity Relationships of N-Aryl 6-Aminoquinoxalines as Potent PFKFB3 Kinase Inhibitors.

Boutard, N., Bialas, A., Sabiniarz, A., Guzik, P., Banaszak, K., Biela, A., Bien, M., Buda, A., Bugaj, B., Cieluch, E., Cierpich, A., Dudek, L., Eggenweiler, H.M., Fogt, J., Gaik, M., Gondela, A., Jakubiec, K., Jurzak, M., Kitlinska, A., Kowalczyk, P., Kujawa, M., Kwiecinska, K., Les, M., Lindemann, R., Maciuszek, M., Mikulski, M., Niedziejko, P., Obara, A., Pawlik, H., Rzymski, T., Sieprawska-Lupa, M., Sowinska, M., Szeremeta-Spisak, J., Stachowicz, A., Tomczyk, M.M., Wiklik, K., Wloszczak, L., Ziemianska, S., Zarebski, A., Brzozka, K., Nowak, M., Fabritius, C.H.

(2019) ChemMedChem 14: 169-181

• PubMed: 30378281 
• DOI: https://doi.org/10.1002/cmdc.201800569
• Primary Citation Related Structures: 
  6HVH, 6HVI, 6HVJ


• PubMed Abstract: 
  

  Energy and biomass production in cancer cells are largely supported by aerobic glycolysis in what is called the Warburg effect. The process is regulated by key enzymes, among which phosphofructokinase PFK-2 plays a significant role by producing fructose-2,6-biphosphate; the most potent activator of the glycolysis rate-limiting step performed by phosphofructokinase PFK-1. Herein, the synthesis, biological evaluation and structure-activity relationship of novel inhibitors of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3), which is the ubiquitous and hypoxia-induced isoform of PFK-2, are reported. X-ray crystallography and docking were instrumental in the design and optimisation of a series of N-aryl 6-aminoquinoxalines. The most potent representative, N-(4-methanesulfonylpyridin-3-yl)-8-(3-methyl-1-benzothiophen-5-yl)quinoxalin-6-amine, displayed an IC ₅₀ of 14 nm for the target and an IC ₅₀ of 0.49 μm for fructose-2,6-biphosphate production in human colon carcinoma HCT116 cells. This work provides a new entry in the field of PFKFB3 inhibitors with potential for development in oncology.

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Organizational Affiliation: 
• Selvita S.A., Bobrzyńskiego 14, 30-348, Kraków, Poland.
Current address: Almac Group, 20 Seagoe Industrial Estate, Craigavon, BT63 5QD, UK.
Current address: Grupa Azoty S.A., Kwiatkowskiego 8, 33-100, Tarnów, Poland.
Medicinal Chemistry, Merck Biopharma, Merck KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany.
Current address: Max Planck Research Group at the Małopolska Centre of Biotechnology, Jagiellonian University, Krakow, Poland.
Discovery Pharmacology, Merck Biopharma, Merck KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany.
Current address: Captor Therapeutics, Duńska 11, 54-427, Wrocław, Poland.
Translational Innovation Platform Oncology, Merck Biopharma, Merck KGaA, Frankfurter Straße 250, 64293, Darmstadt, Germany.
Current address: LifeArc, Accelerator Building, Open Innovation Campus, Stevenage, SG1 2FX, UK.
Current address: Katedra Chemii Organicznej, Bioorganicznej I Biotechnologii, Ul. B. Krzywoustego 4, P., 18/N1, 44-100, Gliwice, Poland.
Current address: Grupa Adamed, Pieńków 149, 05-152, Czosnów, Poland.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: homology

Macromolecule Content 

• Total Structure Weight: 60.82 kDa 
• Atom Count: 4,021 
• Modeled Residue Count: 433 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3	A	520	Homo sapiens	Mutation(s): 0  Gene Names: PFKFB3 EC: 2.7.1.105 (PDB Primary Data), 3.1.3.46 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for Q16875 (Homo sapiens) Explore Q16875  Go to UniProtKB:  Q16875
PHAROS:  Q16875 GTEx:  ENSG00000170525

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GV5	B [auth A]	8-[3-(dimethylamino)phenyl]-~{N}-(4-methylsulfonylpyridin-3-yl)quinoxalin-6-amine C22 H21 N5 O2 S MGSNILVOZHNEMV-UHFFFAOYSA-N
F6P	D [auth A]	6-O-phosphono-beta-D-fructofuranose C6 H13 O9 P BGWGXPAPYGQALX-ARQDHWQXSA-N
FLC	E [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K
POP	C [auth A]	PYROPHOSPHATE 2- H2 O7 P2 XPPKVPWEQAFLFU-UHFFFAOYSA-L
DMS	F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.96 Å
• R-Value Free:  0.208 (Depositor), 0.215 (DCC) 
• R-Value Work:  0.186 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.187 (Depositor) 

Space Group: P 6₅ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.036	α = 90
b = 103.036	β = 90
c = 255.012	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-11-14 
Deposition Author(s): Banaszak, K., Sowinska, M., Gondela, A., Fabritius, C.H., Nowak, M.

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Funding Organization	Location	Grant Number
European Regional Development Fund		POIG.01.04.00-12-120/12-00

Revision History  

• Version 1.0: 2018-11-14
  Type: Initial release
  
• Version 1.1: 2019-01-16
  Changes: Data collection, Database references
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2024-05-15
  Changes: Data collection, Database references, Structure summary