6IBZ

Human PFKFB3 in complex with a N-Aryl 6-Aminoquinoxaline inhibitor 7

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


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


Literature

Synthesis of amide and sulfonamide substituted N-aryl 6-aminoquinoxalines as PFKFB3 inhibitors with improved physicochemical properties.

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) Bioorg Med Chem Lett 29: 646-653

  • DOI: https://doi.org/10.1016/j.bmcl.2018.12.034
  • Primary Citation of Related Structures:  
    6IBX, 6IBY, 6IBZ, 6IC0

  • PubMed Abstract: 

    • In oncology, the "Warburg effect" describes the elevated production of energy by glycolysis in cancer cells. The ubiquitous and hypoxia-induced 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) plays a noteworthy role in the regulation of glycolysis by producing fructose-2,6-biphosphate (F-2,6-BP), a potent activator of the glycolysis rate-limiting phosphofructokinase PFK-1 ...

    In oncology, the "Warburg effect" describes the elevated production of energy by glycolysis in cancer cells. The ubiquitous and hypoxia-induced 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 3 (PFKFB3) plays a noteworthy role in the regulation of glycolysis by producing fructose-2,6-biphosphate (F-2,6-BP), a potent activator of the glycolysis rate-limiting phosphofructokinase PFK-1. Series of amides and sulfonamides derivatives based on a N-aryl 6-aminoquinoxaline scaffold were synthesized and tested for their inhibition of PFKFB3 in vitro in a biochemical assay as well as in HCT116 cells. The carboxamide series displayed satisfactory kinetic solubility and metabolic stability, and within this class, potent lead compounds with low nanomolar activity have been identified with a suitable profile for further in vivo evaluation.

    Organizational Affiliation: 

    Selvita S.A., Bobrzyńskiego, 14, 30-338 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 3431Homo 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 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HAW
Query on HAW
Download Ideal Coordinates CCD File 
D [auth A]2-[[8-(1-methylindol-6-yl)quinoxalin-6-yl]amino]-~{N}-(pyrimidin-5-ylmethyl)benzenesulfonamide
C28 H23 N7 O2 S
FHKKLQIBTXYWGR-UHFFFAOYSA-N		 Ligand Interaction
F6P
Query on F6P
Download Ideal Coordinates CCD File 
E [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 
C [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K		 Ligand Interaction
PO4
Query on PO4
Download Ideal Coordinates CCD File 
B [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
HAW Binding MOAD:  6IBZ IC50: 22 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.44 Å
  • R-Value Free: 0.234 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.046α = 90
b = 103.046β = 90
c = 253.938γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


View more in-depth experimental data
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: 2019-01-23
    Type: Initial release
  • Version 1.1: 2019-02-13
    Changes: Data collection, Database references
  • Version 1.2: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary