4G1N

PKM2 in complex with an activator


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Small Molecule Activation of PKM2 in Cancer Cells Induces Serine Auxotrophy.

Kung, C.Hixon, J.Choe, S.Marks, K.Gross, S.Murphy, E.Delabarre, B.Cianchetta, G.Sethumadhavan, S.Wang, X.Yan, S.Gao, Y.Fang, C.Wei, W.Jiang, F.Wang, S.Qian, K.Saunders, J.Driggers, E.Woo, H.K.Kunii, K.Murray, S.Yang, H.Yen, K.Liu, W.Cantley, L.C.Vander Heiden, M.G.Su, S.M.Jin, S.Salituro, F.G.Dang, L.

(2012) Chem Biol 19: 1187-1198

  • DOI: https://doi.org/10.1016/j.chembiol.2012.07.021
  • Primary Citation of Related Structures:  
    4G1N

  • PubMed Abstract: 

    Proliferating tumor cells use aerobic glycolysis to support their high metabolic demands. Paradoxically, increased glycolysis is often accompanied by expression of the lower activity PKM2 isoform, effectively constraining lower glycolysis. Here, we report the discovery of PKM2 activators with a unique allosteric binding mode. Characterization of how these compounds impact cancer cells revealed an unanticipated link between glucose and amino acid metabolism. PKM2 activation resulted in a metabolic rewiring of cancer cells manifested by a profound dependency on the nonessential amino acid serine for continued cell proliferation. Induction of serine auxotrophy by PKM2 activation was accompanied by reduced carbon flow into the serine biosynthetic pathway and increased expression of high affinity serine transporters. These data support the hypothesis that PKM2 expression confers metabolic flexibility to cancer cells that allows adaptation to nutrient stress.


  • Organizational Affiliation

    Agios Pharmaceuticals, 38 Sidney Street, Cambridge, MA 02139, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Pyruvate kinase isozymes M1/M2
A, B, C, D
518Homo sapiensMutation(s): 0 
Gene Names: PKM2OIP3PK2PK3PKM
EC: 2.7.1.40
UniProt & NIH Common Fund Data Resources
Find proteins for P14618 (Homo sapiens)
Explore P14618 
Go to UniProtKB:  P14618
PHAROS:  P14618
GTEx:  ENSG00000067225 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP14618
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NZT
Query on NZT

Download Ideal Coordinates CCD File 
G [auth A],
N [auth D]
N-(4-{[4-(pyrazin-2-yl)piperazin-1-yl]carbonyl}phenyl)quinoline-8-sulfonamide
C24 H22 N6 O3 S
BNGHGURIVRPDJB-UHFFFAOYSA-N
OXL
Query on OXL

Download Ideal Coordinates CCD File 
E [auth A],
H [auth B],
J [auth C],
L [auth D]
OXALATE ION
C2 O4
MUBZPKHOEPUJKR-UHFFFAOYSA-L
MG
Query on MG

Download Ideal Coordinates CCD File 
F [auth A],
I [auth B],
K [auth C],
M [auth D]
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.211 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.118α = 90
b = 94.141β = 99.39
c = 146.149γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
SCALEPACKdata scaling
PHASESphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-10-10
    Type: Initial release
  • Version 1.1: 2024-02-28
    Changes: Data collection, Database references, Derived calculations