5X1W

PKM2 in complex with compound 5


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.237 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery and structure-guided fragment-linking of 4-(2,3-dichlorobenzoyl)-1-methyl-pyrrole-2-carboxamide as a pyruvate kinase M2 activator

Matsui, Y.Yasumatsu, I.Asahi, T.Kitamura, T.Kanai, K.Ubukata, O.Hayasaka, H.Takaishi, S.Hanzawa, H.Katakura, S.

(2017) Bioorg. Med. Chem. 25: 3540-3546

  • DOI: 10.1016/j.bmc.2017.05.004
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Tumor cells switch glucose metabolism to aerobic glycolysis by expressing the pyruvate kinase M2 isoform (PKM2) in a low active form, providing glycolytic intermediates as building blocks for biosynthetic processes, and thereby supporting cell prolif ...

    Tumor cells switch glucose metabolism to aerobic glycolysis by expressing the pyruvate kinase M2 isoform (PKM2) in a low active form, providing glycolytic intermediates as building blocks for biosynthetic processes, and thereby supporting cell proliferation. Activation of PKM2 should invert aerobic glycolysis to an oxidative metabolism and prevent cancer growth. Thus, PKM2 has gained attention as a promising cancer therapy target. To obtain novel PKM2 activators, we conducted a high-throughput screening (HTS). Among several hit compounds, a fragment-like hit compound with low potency but high ligand efficiency was identified. Two molecules of the hit compound bound at one activator binding site, and the molecules were linked based on the crystal structure. Since this linkage succeeded in maintaining the original position of the hit compound, the obtained compound exhibited highly improved potency in an in vitro assay. The linked compound also showed PKM2 activating activity in a cell based assay, and cellular growth inhibition of the A549 cancer cell line. Discovery of this novel scaffold and binding mode of the linked compound provides a valuable platform for the structure-guided design of PKM2 activators.


    Organizational Affiliation

    Daiichi Sankyo RD Novare Co., Ltd., 1-16-13, Kita-Kasai, Edogawa-ku, Tokyo 134-8630, Japan. Electronic address: matsui.yumi.gk@rdn.daiichisankyo.co.jp.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pyruvate kinase PKM
A, B, C, D
550Homo sapiensMutation(s): 0 
Gene Names: PKM (OIP3, PK2, PK3, PKM2)
EC: 2.7.1.40
Find proteins for P14618 (Homo sapiens)
Go to Gene View: PKM
Go to UniProtKB:  P14618
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
7Y0
Query on 7Y0

Download SDF File 
Download CCD File 
B, C
4-[2,3-bis(chloranyl)phenyl]carbonyl-N-[2-[[4-[2,3-bis(chloranyl)phenyl]carbonyl-1-methyl-pyrrol-2-yl]carbonylamino]ethyl]-1-methyl-pyrrole-2-carboxamide
C28 H22 Cl4 N4 O4
JORSMLRHZLRFBN-UHFFFAOYSA-N
 Ligand Interaction
FBP
Query on FBP

Download SDF File 
Download CCD File 
A, B, C, D
BETA-FRUCTOSE-1,6-DIPHOSPHATE
FRUCTOSE-1,6-BISPHOSPHATE
C6 H14 O12 P2
RNBGYGVWRKECFJ-ARQDHWQXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.237 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 80.823α = 90.00
b = 153.486β = 103.52
c = 94.207γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSphasing
REFMACrefinement
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-05-31
    Type: Initial release