6HVI

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


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

  • DOI: https://doi.org/10.1002/cmdc.201800569
  • Primary Citation of 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 ...

    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.

    Organizational Affiliation: 

    Selvita S.A., Bobrzyńskiego 14, 30-348, Kraków, Poland.



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3520Homo sapiensMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16875
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GV5
Query on GV5
Download Ideal Coordinates CCD File 
B [auth A]8-[3-(dimethylamino)phenyl]-~{N}-(4-methylsulfonylpyridin-3-yl)quinoxalin-6-amine
C22 H21 N5 O2 S
MGSNILVOZHNEMV-UHFFFAOYSA-N		 Ligand Interaction
F6P
Query on F6P
Download Ideal Coordinates CCD File 
D [auth A]6-O-phosphono-beta-D-fructofuranose
C6 H13 O9 P
BGWGXPAPYGQALX-ARQDHWQXSA-N		 Ligand Interaction
FLC
Query on FLC
Download Ideal Coordinates CCD File 
E [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K		 Ligand Interaction
POP
Query on POP
Download Ideal Coordinates CCD File 
C [auth A]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L		 Ligand Interaction
DMS
Query on DMS
Download Ideal Coordinates CCD File 
F [auth A]DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
GV5 Binding MOAD:  6HVI IC50: 380 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.96 Å
  • R-Value Free: 0.208 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.187 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.036α = 90
b = 103.036β = 90
c = 255.012γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
European Regional Development FundPOIG.01.04.00-12-120/12-00

Revision History  (Full details and data files)

  • 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