6Q0D

CRYSTAL STRUCTURE OF LDHA IN COMPLEX WITH COMPOUND NCGC00384414-01 AT 2.05 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Pyrazole-Based Lactate Dehydrogenase Inhibitors with Optimized Cell Activity and Pharmacokinetic Properties.

Rai, G.Urban, D.J.Mott, B.T.Hu, X.Yang, S.M.Benavides, G.A.Johnson, M.S.Squadrito, G.L.Brimacombe, K.R.Lee, T.D.Cheff, D.M.Zhu, H.Henderson, M.J.Pohida, K.Sulikowski, G.A.Dranow, D.M.Kabir, M.Shah, P.Padilha, E.Tao, D.Fang, Y.Christov, P.P.Kim, K.Jana, S.Muttil, P.Anderson, T.Kunda, N.K.Hathaway, H.J.Kusewitt, D.F.Oshima, N.Cherukuri, M.Davies, D.R.Norenberg, J.P.Sklar, L.A.Moore, W.J.Dang, C.V.Stott, G.M.Neckers, L.Flint, A.J.Darley-Usmar, V.M.Simeonov, A.Waterson, A.G.Jadhav, A.Hall, M.D.Maloney, D.J.

(2020) J Med Chem 63: 10984-11011

  • DOI: 10.1021/acs.jmedchem.0c00916
  • Primary Citation of Related Structures:  
    6Q13, 6Q0D

  • PubMed Abstract: 
  • Lactate dehydrogenase (LDH) catalyzes the conversion of pyruvate to lactate, with concomitant oxidation of NADH as the final step in the glycolytic pathway. Glycolysis plays an important role in the metabolic plasticity of cancer cells and has long b ...

    Lactate dehydrogenase (LDH) catalyzes the conversion of pyruvate to lactate, with concomitant oxidation of NADH as the final step in the glycolytic pathway. Glycolysis plays an important role in the metabolic plasticity of cancer cells and has long been recognized as a potential therapeutic target. Thus, potent, selective inhibitors of LDH represent an attractive therapeutic approach. However, to date, pharmacological agents have failed to achieve significant target engagement in vivo, possibly because the protein is present in cells at very high concentrations. We report herein a lead optimization campaign focused on a pyrazole-based series of compounds, using structure-based design concepts, coupled with optimization of cellular potency, in vitro drug-target residence times, and in vivo PK properties, to identify first-in-class inhibitors that demonstrate LDH inhibition in vivo. The lead compounds, named NCATS-SM1440 (43) and NCATS-SM1441 (52) possess desirable attributes for further studying the effect of in vivo LDH inhibition. .


    Organizational Affiliation

    Department of Organic Chemistry, University of Duisburg-Essen, Duisburg, Germany. c.ottmann@tue.nl.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
L-lactate dehydrogenase A chainABCDEF332Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download CCD File 
A, B, C, D, E, F
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
 Ligand Interaction
P8M
Query on P8M

Download CCD File 
A, B, C, D, E, F
2-{3-[3-(cyclopentylethynyl)-4-fluorophenyl]-5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-1H-pyrazol-1-yl}-1,3-thiazole-4-carboxylic acid
C31 H28 F2 N4 O4 S2
KTCLNOGFWLXRFB-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B, C, D, E, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
GOL
Query on GOL

Download CCD File 
B, C, E, F
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.184 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 212.04α = 90
b = 128.07β = 119.35
c = 104.14γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2020-09-23
    Type: Initial release
  • Version 1.1: 2020-10-07
    Changes: Database references
  • Version 1.2: 2020-10-21
    Changes: Database references