4I9U

Crystal structure of rabbit LDHA in complex with a fragment inhibitor AP26256


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Fragment growing and linking lead to novel nanomolar lactate dehydrogenase inhibitors.

Kohlmann, A.Zech, S.G.Li, F.Zhou, T.Squillace, R.M.Commodore, L.Greenfield, M.T.Lu, X.Miller, D.P.Huang, W.S.Qi, J.Thomas, R.M.Wang, Y.Zhang, S.Dodd, R.Liu, S.Xu, R.Xu, Y.Miret, J.J.Rivera, V.Clackson, T.Shakespeare, W.C.Zhu, X.Dalgarno, D.C.

(2013) J.Med.Chem. 56: 1023-1040

  • DOI: 10.1021/jm3014844
  • Primary Citation of Related Structures:  4I8X, 4I9H, 4I9N

  • PubMed Abstract: 
  • Lactate dehydrogenase A (LDH-A) catalyzes the interconversion of lactate and pyruvate in the glycolysis pathway. Cancer cells rely heavily on glycolysis instead of oxidative phosphorylation to generate ATP, a phenomenon known as the Warburg effect. T ...

    Lactate dehydrogenase A (LDH-A) catalyzes the interconversion of lactate and pyruvate in the glycolysis pathway. Cancer cells rely heavily on glycolysis instead of oxidative phosphorylation to generate ATP, a phenomenon known as the Warburg effect. The inhibition of LDH-A by small molecules is therefore of interest for potential cancer treatments. We describe the identification and optimization of LDH-A inhibitors by fragment-based drug discovery. We applied ligand based NMR screening to identify low affinity fragments binding to LDH-A. The dissociation constants (K(d)) and enzyme inhibition (IC(50)) of fragment hits were measured by surface plasmon resonance (SPR) and enzyme assays, respectively. The binding modes of selected fragments were investigated by X-ray crystallography. Fragment growing and linking, followed by chemical optimization, resulted in nanomolar LDH-A inhibitors that demonstrated stoichiometric binding to LDH-A. Selected molecules inhibited lactate production in cells, suggesting target-specific inhibition in cancer cell lines.


    Organizational Affiliation

    ARIAD Pharmaceuticals, Inc., 26 Landsdowne Street, Cambridge, Massachusetts 02139, USA. anna.kohlmann@ariad.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-lactate dehydrogenase A chain
A, B, C, D, E, F, G, H
331Oryctolagus cuniculusGene Names: LDHA
EC: 1.1.1.27
Find proteins for P13491 (Oryctolagus cuniculus)
Go to Gene View: LDHA
Go to UniProtKB:  P13491
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1E7
Query on 1E7

Download SDF File 
Download CCD File 
A, B, C, D, E, F, G, H
6-({2-[(5-chloro-2-methoxyphenyl)amino]-2-oxoethyl}sulfanyl)pyridine-3-carboxylic acid
C15 H13 Cl N2 O4 S
XMYZLTXLDRMRAM-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1E7Kd: 137000 nM (93) BINDINGDB
1E7IC50: 770000 nM (93) BINDINGDB
1E7Kd: 137000 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 83.690α = 90.00
b = 138.740β = 94.82
c = 138.170γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
CNSphasing
HKL-2000data scaling
StructureStudiodata collection
PDB_EXTRACTdata extraction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-01-23
    Type: Initial release
  • Version 1.1: 2013-02-27
    Type: Database references