4I9U

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 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, 4I9U, 4I9N, 4I9H

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-lactate dehydrogenase A chainABCDEFGH331Oryctolagus cuniculusMutation(s): 0 
Gene Names: LDHA
EC: 1.1.1.27
Find proteins for P13491 (Oryctolagus cuniculus)
Explore P13491 
Go to UniProtKB:  P13491
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1E7
Query on 1E7

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  BindingDB
1E7IC50:  770000   nM  BindingDB
1E7Kd:  137000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.273 
  • R-Value Work: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.69α = 90
b = 138.74β = 94.82
c = 138.17γ = 90
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
StructureStudiodata collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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