4AJJ

rat LDHA in complex with 2-((3,4-dimethoxyphenyl)methyl))propanedioic acid and N-(2-methyl-1,3-benzothiazol-6-yl)-3-ureido-propanamide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 

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:  
    4AJ1, 4AJ2, 4AJ4, 4AJN, 4AJO, 4AJP, 4AJE, 4AJH, 4AJI, 4AJJ

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-LACTATE DEHYDROGENASE A CHAINABCD331Rattus norvegicusMutation(s): 0 
Gene Names: LdhaLdh-1Ldh1
EC: 1.1.1.27
Find proteins for P04642 (Rattus norvegicus)
Explore P04642 
Go to UniProtKB:  P04642
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
88S
Query on 88S

Download CCD File 
A, B, C, D
N-(2-METHYL-1,3-BENZOTHIAZOL-6-YL)-3-UREIDO-PROPANAMIDE
C12 H14 N4 O2 S
OVXHZNUBLPBIEB-UHFFFAOYSA-N
 Ligand Interaction
88R
Query on 88R

Download CCD File 
B, C
2-((3,4-DIMETHOXYPHENYL)METHYL))PROPANEDIOIC ACID
C12 H14 O6
NQKOQSKMBSAXTD-UHFFFAOYSA-N
 Ligand Interaction
MLI
Query on MLI

Download CCD File 
A, D
MALONATE ION
C3 H2 O4
OFOBLEOULBTSOW-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
C
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download CCD File 
C
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
88RKd:  280000   nM  Binding MOAD
88RIC50:  500000   nM  BindingDB
88SKd:  770000   nM  Binding MOAD
88RKd:  280000   nM  BindingDB
88SKd:  770000   nM  BindingDB
88SIC50:  500000   nM  BindingDB
88RKd:  1000000   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.75 Å
  • R-Value Free: 0.173 
  • R-Value Work: 0.144 
  • R-Value Observed: 0.146 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.141α = 90
b = 81.892β = 96.06
c = 128.986γ = 90
Software Package:
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

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