4AJN

rat LDHA in complex with 2-((4-(2-((3-((2-methyl-1,3-benzothiazol-6- yl)amino)-3-oxo-propyl)carbamoylamino)ethyl)phenyl)methyl) propanedioic acid


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

The Design and Synthesis of Novel Lactate Dehydrogenase a Inhibitors by Fragment-Based Lead Generation

Ward, R.Brassington, C.Breeze, A.L.Caputo, A.Critchlow, S.Davies, G.Goodwin, L.Hassall, G.Greenwood, R.Holdgate, G.Mrosek, M.Norman, R.A.Pearson, S.Tart, J.Tucker, J.A.Vogtherr, M.Whittaker, D.Wingfield, J.Winter, J.Hudson, K.

(2012) J.Med.Chem. 55: 3285

  • DOI: 10.1021/jm201734r
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lactate dehydrogenase A (LDHA) catalyzes the conversion of pyruvate to lactate, utilizing NADH as a cofactor. It has been identified as a potential therapeutic target in the area of cancer metabolism. In this manuscript we report our progress using f ...

    Lactate dehydrogenase A (LDHA) catalyzes the conversion of pyruvate to lactate, utilizing NADH as a cofactor. It has been identified as a potential therapeutic target in the area of cancer metabolism. In this manuscript we report our progress using fragment-based lead generation (FBLG), assisted by X-ray crystallography to develop small molecule LDHA inhibitors. Fragment hits were identified through NMR and SPR screening and optimized into lead compounds with nanomolar binding affinities via fragment linking. Also reported is their modification into cellular active compounds suitable for target validation work.


    Organizational Affiliation

    Oncology and Discovery Sciences iMEDs, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. richard.a.ward@astrazeneca.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-LACTATE DEHYDROGENASE A CHAIN
A, B, C, D
331Rattus norvegicusMutation(s): 0 
Gene Names: Ldha (Ldh-1, Ldh1)
EC: 1.1.1.27
Find proteins for P04642 (Rattus norvegicus)
Go to UniProtKB:  P04642
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
88V
Query on 88V

Download SDF File 
Download CCD File 
A, B, C, D
(4-{2-[({3-[(2-METHYL-1,3-BENZOTHIAZOL-6-YL)AMINO]-3-OXOPROPYL}CARBAMOYL)AMINO]ETHYL}BENZYL)PROPANEDIOIC ACID
C24 H26 N4 O6 S
GADNEHRFYQNKCC-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
88VIC50: 1900 nM (100) BINDINGDB
88VKd: 69 nM (100) BINDINGDB
88VKd: 69 nM BINDINGMOAD
88VKd: 69 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.179 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 62.222α = 90.00
b = 82.728β = 96.23
c = 129.481γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
REFMACrefinement
SCALAdata scaling
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-04-25
    Type: Other
  • Version 1.2: 2018-04-04
    Type: Data collection