6SBU

X-ray Structure of Human LDHA with an Allosteric Inhibitor (Compound 3)

• PDB DOI: https://doi.org/10.2210/pdb6SBU/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2019-07-22 Released: 2020-06-10 
• Deposition Author(s): Friberg, A., Puetter, V., Nguyen, D., Rehwinkel, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.244 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Starting Model: experimental

Literature

Structural Evidence for Isoform-Selective Allosteric Inhibition of Lactate Dehydrogenase A.

Friberg, A., Rehwinkel, H., Nguyen, D., Putter, V., Quanz, M., Weiske, J., Eberspacher, U., Heisler, I., Langer, G.

(2020) ACS Omega 5: 13034-13041

• PubMed: 32548488 
• DOI: https://doi.org/10.1021/acsomega.0c00715
• Primary Citation of Related Structures:  
  6SBU, 6SBV


• PubMed Abstract: 
  

  Lactate dehydrogenase A (LDHA) is frequently overexpressed in tumors, thereby sustaining high glycolysis rates, tumor growth, and chemoresistance. High-throughput screening resulted in the identification of phthalimide and dibenzofuran derivatives as novel lactate dehydrogenase inhibitors, selectively inhibiting the activity of the LDHA isoenzyme. Cocrystallization experiments confirmed target engagement in addition to demonstrating binding to a novel allosteric binding site present in all four LDHA subunits of the LDH5 homotetramer.

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Organizational Affiliation: 

Bayer AG, Pharmaceuticals, R&D, Müllerstrasse 178, 13342 Berlin, Germany.

Biological Assembly 1  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly 2  

Global Symmetry: Dihedral - D2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 298.14 kDa 
• Atom Count: 20,754 
• Modelled Residue Count: 2,624 
• Deposited Residue Count: 2,656 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase A chain	A, B, C, D, E, F, G, H	332	Homo sapiens	Mutation(s): 0  Gene Names: LDHA, PIG19 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

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAI	J [auth A], O [auth E]	1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE C21 H29 N7 O14 P2 BOPGDPNILDQYTO-NNYOXOHSSA-N
L5N (Subject of Investigation/LOI)	I [auth A], K [auth B], L [auth C], M [auth D], N [auth E], P [auth F], Q [auth G], R [auth H]	4-[[4-[(5-chloranylthiophen-2-yl)carbonylamino]-1,3-bis(oxidanylidene)isoindol-2-yl]methyl]benzoic acid C21 H13 Cl N2 O5 S IOFCJSIYHLICRV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.91 Å
• R-Value Free: 0.244 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.445	α = 90
b = 143.853	β = 90
c = 311.225	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
Coot	model building

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-06-10 
Deposition Author(s): Friberg, A., Puetter, V., Nguyen, D., Rehwinkel, H.

Revision History  

• Version 1.0: 2020-06-10
  Type: Initial release
  
• Version 1.1: 2020-07-01
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Database references, Refinement description