5W8H

Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 11


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.147 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Discovery and Optimization of Potent, Cell-Active Pyrazole-Based Inhibitors of Lactate Dehydrogenase (LDH).

Rai, G.Brimacombe, K.R.Mott, B.T.Urban, D.J.Hu, X.Yang, S.M.Lee, T.D.Cheff, D.M.Kouznetsova, J.Benavides, G.A.Pohida, K.Kuenstner, E.J.Luci, D.K.Lukacs, C.M.Davies, D.R.Dranow, D.M.Zhu, H.Sulikowski, G.Moore, W.J.Stott, G.M.Flint, A.J.Hall, M.D.Darley-Usmar, V.M.Neckers, L.M.Dang, C.V.Waterson, A.G.Simeonov, A.Jadhav, A.Maloney, D.J.

(2017) J. Med. Chem. 60: 9184-9204

  • DOI: 10.1021/acs.jmedchem.7b00941
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the discovery and medicinal chemistry optimization of a novel series of pyrazole-based inhibitors of human lactate dehydrogenase (LDH). Utilization of a quantitative high-throughput screening paradigm facilitated hit identification, while s ...

    We report the discovery and medicinal chemistry optimization of a novel series of pyrazole-based inhibitors of human lactate dehydrogenase (LDH). Utilization of a quantitative high-throughput screening paradigm facilitated hit identification, while structure-based design and multiparameter optimization enabled the development of compounds with potent enzymatic and cell-based inhibition of LDH enzymatic activity. Lead compounds such as 63 exhibit low nM inhibition of both LDHA and LDHB, submicromolar inhibition of lactate production, and inhibition of glycolysis in MiaPaCa2 pancreatic cancer and A673 sarcoma cells. Moreover, robust target engagement of LDHA by lead compounds was demonstrated using the cellular thermal shift assay (CETSA), and drug-target residence time was determined via SPR. Analysis of these data suggests that drug-target residence time (off-rate) may be an important attribute to consider for obtaining potent cell-based inhibition of this cancer metabolism target.


    Organizational Affiliation

    National Center for Advancing Translational Sciences, National Institutes of Health , 9800 Medical Center Drive, Rockville, Maryland 20850, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
L-lactate dehydrogenase A chain
A, B, C, D
332Homo sapiensMutation(s): 0 
Gene Names: LDHA
EC: 1.1.1.27
Find proteins for P00338 (Homo sapiens)
Go to Gene View: LDHA
Go to UniProtKB:  P00338
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

Download SDF File 
Download CCD File 
A, B, D
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
C, D
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
9Y1
Query on 9Y1

Download SDF File 
Download CCD File 
A, B, C
2-[3-(4-fluorophenyl)-5-(trifluoromethyl)-1H-pyrazol-1-yl]-1,3-thiazole-4-carboxylic acid
C14 H7 F4 N3 O2 S
QJOXPOLQKMNMLN-UHFFFAOYSA-N
 Ligand Interaction
MLA
Query on MLA

Download SDF File 
Download CCD File 
B
MALONIC ACID
DICARBOXYLIC ACID C3; PROPANEDIOLIC ACID; METHANEDICARBOXYLIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

Download SDF File 
Download CCD File 
A, B, D
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.181 
  • R-Value Work: 0.147 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 167.730α = 90.00
b = 81.210β = 118.22
c = 120.650γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
XDSdata reduction
PDB_EXTRACTdata extraction
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-01-17
    Type: Initial release