8QDE | pdb_00008qde

Crystal structure of a truncated human L-Lactate Dehydrogenase B protein in complex with NADH and oxamate


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free: 
    0.310 (Depositor), 0.311 (DCC) 
  • R-Value Work: 
    0.231 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 
    0.235 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history


Literature

Unveiling the enzymatic activity of a dimeric LDH isoform and its implications for allosteric inhibition strategies.

Nadal-Bufi, F.Van Gysel, M.Brustenga, C.Savoyen, P.Mathieu, C.Gobert, A.Sonveaux, P.Spillier, Q.Fillet, M.Wouters, J.Frederick, R.

(2025) Protein Sci 34: e70367-e70367

  • DOI: https://doi.org/10.1002/pro.70367
  • Primary Citation of Related Structures:  
    8QDE

  • PubMed Abstract: 

    Lactate dehydrogenase (LDH) is a key enzyme in cancer metabolism, with isoforms LDH5 and LDH1 supporting glycolysis and oxidative lactate metabolism, respectively. While the development of competitive LDH inhibitors has faced diverse challenges, allosteric strategies targeting LDH tetramerization have recently attracted increasing attention. To further explore this alternative, we investigated the factors influencing LDH tetramerization and enzymatic activity using a truncated form of human LDH-B (LDHBtr), which was reported to exist predominantly as a dimer. Unexpectedly, LDHBtr exhibited measurable activity at high concentrations, correlating with increased protein stability and a structural transition to the tetrameric form. Preincubation with NADH further enhanced LDHBtr activity, stability, and self-association, consistent with cofactor-promoted tetramer assembly. Crystallographic studies confirmed the tetrameric structure of LDHBtr bound to NADH. Furthermore, reported LDH allosteric inhibitors, including cGmC9 and fluoxetine, preferentially inhibited LDHBtr compared to the native LDHB, by preventing tetramer formation. Overall, this work highlights the central role of tetramerization in regulating LDH activity, and the therapeutic potential of targeting this process. It also establishes LDHBtr as a valuable tool for screening tetramerization disruptors, paving the way for next-generation LDH inhibitors to target cancer metabolism.


  • Organizational Affiliation
    • Medicinal Chemistry Research Group (CMFA), Louvain Drug Research Institute (LDRI), Université catholique de Louvain (UCLouvain), Brussels, Belgium.

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
330Homo sapiensMutation(s): 0 
Gene Names: LDHB
EC: 1.1.1.27
UniProt & NIH Common Fund Data Resources
Find proteins for P07195 (Homo sapiens)
Explore P07195 
Go to UniProtKB:  P07195
PHAROS:  P07195
GTEx:  ENSG00000111716 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP07195
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
E [auth A],
K [auth B],
P [auth C],
U [auth D]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
PGE
Query on PGE

Download Ideal Coordinates CCD File 
G [auth A],
N [auth B],
R [auth C]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
M [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
O [auth B]
S [auth C]
H [auth A],
I [auth A],
J [auth A],
O [auth B],
S [auth C],
T [auth C],
W [auth D]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
OXM (Subject of Investigation/LOI)
Query on OXM

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

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.98 Å
  • R-Value Free:  0.310 (Depositor), 0.311 (DCC) 
  • R-Value Work:  0.231 (Depositor), 0.231 (DCC) 
  • R-Value Observed: 0.235 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 71.53α = 90
b = 85.66β = 90
c = 207.1γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
MxCuBEdata collection
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Fonds National de la Recherche Scientifique (FNRS)Belgium--

Revision History  (Full details and data files)

  • Version 1.0: 2024-09-11
    Type: Initial release
  • Version 1.1: 2025-12-17
    Changes: Database references, Structure summary