6HVH

Human PFKFB3 in complex with a N-Aryl 6-Aminoquinoxaline inhibitor 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1002/cmdc.201800569
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Energy and biomass production in cancer cell is 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 fructo ...

    Energy and biomass production in cancer cell is 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. We report herein the synthesis, biological evaluation and structure-activity relationship of novel inhibitors of 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3), the ubiquitous and hypoxia-induced isoform of PFK-2. X-Ray crystallography and docking were instrumental in the design and optimization of a N-aryl 6-aminoquinoxaline series. The most potent representative, compound 69, displayed a 14 nM IC50 on target, and a 0.49 μM IC50 of 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 SA, Discovery Chemistry, Ul. Bobrzyńskiego 14, 30-348, Kraków, POLAND.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3
A
520Homo sapiensMutation(s): 0 
Gene Names: PFKFB3
Find proteins for Q16875 (Homo sapiens)
Go to Gene View: PFKFB3
Go to UniProtKB:  Q16875
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
POP
Query on POP

Download SDF File 
Download CCD File 
A
PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
 Ligand Interaction
GV2
Query on GV2

Download SDF File 
Download CCD File 
A
3-[[8-(1-methylindol-6-yl)quinoxalin-6-yl]amino]-~{N}-(oxan-4-yl)pyridine-4-carboxamide
C28 H26 N6 O2
PNSFFJLFHRNWQC-UHFFFAOYSA-N
 Ligand Interaction
FLC
Query on FLC

Download SDF File 
Download CCD File 
A
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
F6P
Query on F6P

Download SDF File 
Download CCD File 
A
FRUCTOSE-6-PHOSPHATE
C6 H13 O9 P
BGWGXPAPYGQALX-ARQDHWQXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.195 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 103.060α = 90.00
b = 103.060β = 90.00
c = 254.825γ = 120.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


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

Revision History 

  • Version 1.0: 2018-11-14
    Type: Initial release
  • Version 1.1: 2019-01-16
    Type: Data collection, Database references