6Q13

CRYSTAL STRUCTURE OF LDHA IN COMPLEX WITH COMPOUND NCGC00420737-09 AT 2.00 A RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report

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This is version 1.3 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: https://doi.org/10.1021/acs.jmedchem.0c00916
  • Primary Citation of Related Structures:  
    6Q0D, 6Q13

  • PubMed Abstract: 

    Lactate dehydrogenase (LDH) catalyzes the conversion of pyruvate to lactate, with concomitant oxidation of reduced nicotinamide adenine dinucleotide 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

    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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-lactate dehydrogenase A chain
A, B, C, D
332Homo sapiensMutation(s): 0 
Gene Names: LDHAPIG19
EC: 1.1.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P00338 (Homo sapiens)
Explore P00338 
Go to UniProtKB:  P00338
PHAROS:  P00338
GTEx:  ENSG00000134333 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00338
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI
Query on NAI

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
N [auth C],
T [auth D]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
P8V (Subject of Investigation/LOI)
Query on P8V

Download Ideal Coordinates CCD File 
F [auth A],
L [auth B],
O [auth C],
U [auth D]
2-[5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-3-{3-[(5-methylthiophen-2-yl)ethynyl]phenyl}-1H-pyrazol-1-yl]-1,3-thiazole-4-carboxylic acid
C31 H25 F N4 O4 S3
LZIKVHXLVMNROK-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
G [auth A]
H [auth A]
I [auth A]
J [auth A]
M [auth B]
G [auth A],
H [auth A],
I [auth A],
J [auth A],
M [auth B],
P [auth C],
Q [auth C],
R [auth C],
S [auth C],
V [auth D],
W [auth D],
X [auth D],
Y [auth D],
Z [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.169 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 134.8α = 90
b = 94.74β = 90
c = 121.56γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
MoRDaphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.3: 2023-10-11
    Changes: Data collection, Database references, Refinement description