6CEP

Sus scrofa heart L-lactate dehydrogenase ternary complex with NADH and oxamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.4 of the entry. See complete history


Literature

Small molecule cores demonstrate non-competitive inhibition of lactate dehydrogenase.

Andrews, B.A.Dyer, R.B.

(2018) Medchemcomm 9: 1369-1376

  • DOI: https://doi.org/10.1039/c8md00309b
  • Primary Citation of Related Structures:  
    6CEP

  • PubMed Abstract: 

    Lactate dehydrogenase (LDH) has recently garnered attention as an attractive target for cancer therapies, owing to the enzyme's critical role in cellular metabolism. Current inhibition strategies, employing substrate or cofactor analogues, are insufficiently specific for use as pharmaceutical agents. The possibility of allosteric inhibition of LDH was postulated on the basis of theoretical docking studies of a small molecule inhibitor to LDH. The present study examined structural analogues of this proposed inhibitor to gauge its potency and attempt to elucidate the molecular mechanism of action. These analogues display encouraging in vitro inhibition of porcine heart LDH, including micromolar K i values and a maximum inhibition of up to 50% in the steady state. Furthermore, Michaelis-Menten kinetics and fluorescence data both suggest the simple, acetaminophen derivatives are non-competitive in binding to the enzyme. Kinetic comparisons of a panel of increasingly decorated structural analogues imply that the binding is specific, and the small molecule core provides a privileged scaffold for further pharmaceutical development of a novel, allosteric drug.


  • Organizational Affiliation

    Department of Chemistry , Emory University , Atlanta , 30322 , Georgia , USA . Email: briandyer@emory.edu.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
L-lactate dehydrogenase B chain
A, B, C, D
334Sus scrofaMutation(s): 0 
EC: 1.1.1.27
UniProt
Find proteins for P00336 (Sus scrofa)
Explore P00336 
Go to UniProtKB:  P00336
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00336
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAD
Query on NAD

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B],
I [auth C],
K [auth D]
NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C21 H27 N7 O14 P2
BAWFJGJZGIEFAR-NNYOXOHSSA-N
OXM
Query on OXM

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B],
J [auth C],
L [auth D]
OXAMIC ACID
C2 H3 N O3
SOWBFZRMHSNYGE-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.257 
  • R-Value Work: 0.216 
  • R-Value Observed: 0.217 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 60.12α = 90
b = 137.23β = 90
c = 161.34γ = 90
Software Package:
Software NamePurpose
xia2data reduction
DIALSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXrefinement
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM068036-014

Revision History  (Full details and data files)

  • Version 1.0: 2018-06-27
    Type: Initial release
  • Version 1.1: 2019-01-09
    Changes: Data collection, Database references
  • Version 1.2: 2019-02-20
    Changes: Author supporting evidence, Data collection
  • Version 1.3: 2020-01-01
    Changes: Author supporting evidence
  • Version 1.4: 2023-10-04
    Changes: Data collection, Database references, Refinement description