5W8J

Crystal Structure of Lactate Dehydrogenase A in complex with inhibitor compound 29


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 

wwPDB Validation   3D Report Full Report



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:  
    5W8I, 5W8H, 5W8K, 5W8J, 5W8L

  • 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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-lactate dehydrogenase A chainABCD332Homo sapiensMutation(s): 0 
Gene Names: LDHAPIG19
EC: 1.1.1.27
Find proteins for P00338 (Homo sapiens)
Explore P00338 
Go to UniProtKB:  P00338
NIH Common Fund Data Resources
PHAROS  P00338
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9Y7
Query on 9Y7

Download CCD File 
A, B, C, D
2-{3-(3,4-difluorophenyl)-5-hydroxy-4-[(4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid
C20 H14 F2 N4 O5 S2
HADCVZAHKWNLJA-UHFFFAOYSA-N
 Ligand Interaction
MLA
Query on MLA

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A, B, C, D
MALONIC ACID
C3 H4 O4
OFOBLEOULBTSOW-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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

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A, C, D
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
9Y7IC50:  672   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.55 Å
  • R-Value Free: 0.169 
  • R-Value Work: 0.145 
  • R-Value Observed: 0.146 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 168.53α = 90
b = 80.77β = 118.23
c = 121.09γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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