6IBY

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.3 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. 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
MoleculeChains Sequence LengthOrganismDetailsImage
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3428Homo 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
GTEx:  ENSG00000170525 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16875
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HAT
Query on HAT

Download Ideal Coordinates CCD File 
B [auth A]3-[[8-(1-methylindol-6-yl)quinoxalin-6-yl]amino]-~{N}-[(3~{S})-1-methylpyrrolidin-3-yl]pyridine-4-carboxamide
C28 H27 N7 O
JQYNBBAXGSXALE-FQEVSTJZSA-N
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
FLC
Query on FLC

Download Ideal Coordinates CCD File 
D [auth A]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
POP
Query on POP

Download Ideal Coordinates CCD File 
C [auth A]PYROPHOSPHATE 2-
H2 O7 P2
XPPKVPWEQAFLFU-UHFFFAOYSA-L
PO4
Query on PO4

Download Ideal Coordinates CCD File 
G [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
BME
Query on BME

Download Ideal Coordinates CCD File 
F [auth A]BETA-MERCAPTOETHANOL
C2 H6 O S
DGVVWUTYPXICAM-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.232 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.532α = 90
b = 102.532β = 90
c = 253.658γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
European Regional Development Fundunder The Operational Program Innovative Economy, 2007-2013, measure 1.4 (POIG.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
  • Version 1.3: 2024-01-24
    Changes: Data collection, Database references, Refinement description, Structure summary