6ETJ | pdb_00006etj

HUMAN PFKFB3 IN COMPLEX WITH KAN0438241


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 
    0.235 (Depositor), 0.208 (DCC) 
  • R-Value Work: 
    0.192 (Depositor) 
  • R-Value Observed: 
    0.194 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 6ETJ

Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history

Literature

Targeting PFKFB3 radiosensitizes cancer cells and suppresses homologous recombination.

Gustafsson, N.M.S.Farnegardh, K.Bonagas, N.Ninou, A.H.Groth, P.Wiita, E.Jonsson, M.Hallberg, K.Lehto, J.Pennisi, R.Martinsson, J.Norstrom, C.Hollers, J.Schultz, J.Andersson, M.Markova, N.Marttila, P.Kim, B.Norin, M.Olin, T.Helleday, T.

(2018) Nat Commun 9: 3872-3872

  • DOI: https://doi.org/10.1038/s41467-018-06287-x
  • Primary Citation Related Structures: 
    6ETJ

  • PubMed Abstract: 

    The glycolytic PFKFB3 enzyme is widely overexpressed in cancer cells and an emerging anti-cancer target. Here, we identify PFKFB3 as a critical factor in homologous recombination (HR) repair of DNA double-strand breaks. PFKFB3 rapidly relocates into ionizing radiation (IR)-induced nuclear foci in an MRN-ATM-γH2AX-MDC1-dependent manner and co-localizes with DNA damage and HR repair proteins. PFKFB3 relocalization is critical for recruitment of HR proteins, HR activity, and cell survival upon IR. We develop KAN0438757, a small molecule inhibitor that potently targets PFKFB3. Pharmacological PFKFB3 inhibition impairs recruitment of ribonucleotide reductase M2 and deoxynucleotide incorporation upon DNA repair, and reduces dNTP levels. Importantly, KAN0438757 induces radiosensitization in transformed cells while leaving non-transformed cells unaffected. In summary, we identify a key role for PFKFB3 enzymatic activity in HR repair and present KAN0438757, a selective PFKFB3 inhibitor that could potentially be used as a strategy for the treatment of cancer.


  • Organizational Affiliation
    • Science for Life Laboratory, Department of Oncology and Pathology, Karolinska Institutet, 171 21, Stockholm, Sweden. nina.gustafsson@scilifelab.se.

Macromolecule Content 

  • Total Structure Weight: 60.94 kDa 
  • Atom Count: 3,736 
  • Modeled Residue Count: 432 
  • Deposited Residue Count: 520 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence 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
GTEx:  ENSG00000170525 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ16875
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
NEP
Query on NEP
A
L-PEPTIDE LINKINGC6 H10 N3 O5 PHIS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free:  0.235 (Depositor), 0.208 (DCC) 
  • R-Value Work:  0.192 (Depositor) 
  • R-Value Observed: 0.194 (Depositor) 
Space Group: P 65 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 103.774α = 90
b = 103.774β = 90
c = 259.563γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XSCALEdata reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-07
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.2: 2025-04-09
    Changes: Data collection, Database references, Structure summary