6ETJ

HUMAN PFKFB3 IN COMPLEX WITH KAN0438241


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.1 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: 10.1038/s41467-018-06287-x
  • Primary Citation of 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 ...

    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

    Sheffield Cancer Centre, Department of Oncology and Metabolism, University of Sheffield, S10 2RX, Sheffield, UK. t.helleday@sheffield.ac.uk.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase 3A520Homo sapiensMutation(s): 0 
Gene Names: PFKFB3
EC: 2.7.1.105 (PDB Primary Data), 3.1.3.46 (PDB Primary Data)
Find proteins for Q16875 (Homo sapiens)
Explore Q16875 
Go to UniProtKB:  Q16875
NIH Common Fund Data Resources
PHAROS  Q16875
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ADP
Query on ADP

Download CCD File 
A
ADENOSINE-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
XTWYTFMLZFPYCI-KQYNXXCUSA-N
 Ligand Interaction
BWW
Query on BWW

Download CCD File 
A
4-[[3-(5-fluoranyl-2-oxidanyl-phenyl)phenyl]sulfonylamino]-2-oxidanyl-benzoic acid
C19 H14 F N O6 S
DDVUKRHRMBDQTD-UHFFFAOYSA-N
 Ligand Interaction
F6P
Query on F6P

Download CCD File 
A
6-O-phosphono-beta-D-fructofuranose
C6 H13 O9 P
BGWGXPAPYGQALX-ARQDHWQXSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
A
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
NEP
Query on NEP
AL-PEPTIDE LINKINGC6 H10 N3 O5 PHIS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.51 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • 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



Entry History 

Revision History 

  • 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