7M2N | pdb_00007m2n

Crystal structure of Human Lactate Dehydrogenase A with Inhibitor Compound 15


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 
    0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work: 
    0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.212 (Depositor) 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Characterization of CHK-336, A First-in-Class, Liver-Targeted, Small-Molecule Lactate Dehydrogenase Inhibitor for Hyperoxaluria Treatment.

Cox, J.H.Boily, M.O.Caron, A.Sheng, T.Wu, J.Ding, J.Gaudreault, S.Chong, O.Surendradoss, J.Gomez, R.Lester, J.Dumais, V.Li, X.Gumpena, R.Hall, M.D.Waterson, A.G.Stott, G.Flint, A.J.Moore, W.J.Lowther, W.T.Knight, J.Percival, M.D.Tong, V.Oballa, R.Powell, D.A.King, A.J.

(2025) J Am Soc Nephrol 36: 1535-1547

  • DOI: https://doi.org/10.1681/ASN.0000000690
  • Primary Citation of Related Structures:  
    7M2N, 8FW6

  • PubMed Abstract: 

    Primary hyperoxalurias are genetic diseases defined by elevated hepatic oxalate production and higher incidence of kidney stones. Lactate dehydrogenase A catalyzes the final and committed step in hepatic oxalate synthesis and represents a potential therapeutic target for primary hyperoxalurias. CHK-336 is a liver-targeted, small-molecule lactate dehydrogenase A inhibitor with potential to treat diseases associated with elevated oxalate production. Primary hyperoxalurias (PH) 1–3 are genetic diseases defined by elevated hepatic oxalate production and higher incidence of calcium oxalate kidney stones and potentially kidney failure. There are two approved agents available for PH1, and there are no approved therapies for PH2 or PH3. Lactate dehydrogenase A catalyzes the final step in hepatic oxalate synthesis and represents a potential therapeutic target for PH and other forms of hyperoxaluria associated with increased oxalate production. Potent and selective lactate dehydrogenase (LDH) inhibitors with liver-targeted tissue distribution were identified and characterized in enzymatic, cellular, and in vivo models. We identified CHK-336, a novel oral small-molecule that demonstrates potent and selective inhibition of the human LDH enzyme and its activity in hepatocyte assays across multiple species, including hepatocytes isolated from PH1 mice. CHK-336 demonstrated a favorable liver distribution profile in mice, rats, and monkeys that was dependent on hepatic uptake by organic anion-transporting polypeptide transporters and target-mediated drug binding. In a rat pharmacodynamic model, CHK-336 inhibited conversion of 13 C 2 -glycolate to 13 C 2 -oxalate in a dose-dependent manner. In a PH1 mouse model, once-daily oral dosing of CHK-336 produced robust and dose-dependent reductions in urinary oxalate to the normal range. Seven days of treatment with CHK-336 also resulted in a significant reduction in urinary oxalate in a PH2 mouse model. In conclusion, CHK-336 is a potent, liver-targeted, small-molecule LDH inhibitor that suppressed urinary oxalate production in a rat pharmacodynamic model and mouse models of PH1 and PH2.


  • Organizational Affiliation
    • Chinook Therapeutics, Inc., Seattle, Washington.

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
338Homo 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
Expand
  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
YOJ (Subject of Investigation/LOI)
Query on YOJ

Download Ideal Coordinates CCD File 
BB [auth B],
BD [auth D],
EC [auth C],
X [auth A]
5-[(5'-{1-(4-carboxy-1,3-thiazol-2-yl)-5-(cyclopropylmethyl)-4-[(3-fluoro-4-sulfamoylphenyl)methyl]-1H-pyrazol-3-yl}-2'-fluoro[1,1'-biphenyl]-4-yl)oxy]-1H-1,2,3-triazole-4-carboxylic acid
C33 H25 F2 N7 O7 S2
OLGHHCBVTKMRAO-UHFFFAOYSA-N
NAI (Subject of Investigation/LOI)
Query on NAI

Download Ideal Coordinates CCD File 
E [auth A],
JA [auth B],
NB [auth C],
RC [auth D]
1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE
C21 H29 N7 O14 P2
BOPGDPNILDQYTO-NNYOXOHSSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
CB [auth B]
FA [auth A]
IB [auth B]
N [auth A]
RA [auth B]
CB [auth B],
FA [auth A],
IB [auth B],
N [auth A],
RA [auth B],
U [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
AA [auth A]
DD [auth D]
EA [auth A]
F [auth A]
HA [auth B]
AA [auth A],
DD [auth D],
EA [auth A],
F [auth A],
HA [auth B],
HC [auth D],
IA [auth B],
LB [auth C],
NA [auth B],
YA [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
CC [auth C]
DC [auth C]
FB [auth B]
GC [auth C]
M [auth A]
CC [auth C],
DC [auth C],
FB [auth B],
GC [auth C],
M [auth A],
PC [auth D]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AB [auth B]
AC [auth C]
AD [auth D]
BA [auth A]
BC [auth C]
AB [auth B],
AC [auth C],
AD [auth D],
BA [auth A],
BC [auth C],
CA [auth A],
CD [auth D],
DA [auth A],
DB [auth B],
EB [auth B],
ED [auth D],
FC [auth C],
G [auth A],
GA [auth B],
GB [auth B],
H [auth A],
HB [auth B],
I [auth A],
IC [auth D],
J [auth A],
JB [auth B],
JC [auth D],
K [auth A],
KA [auth B],
KB [auth C],
KC [auth D],
L [auth A],
LA [auth B],
LC [auth D],
MA [auth B],
MB [auth C],
MC [auth D],
NC [auth D],
O [auth A],
OA [auth B],
OB [auth C],
OC [auth D],
P [auth A],
PA [auth B],
PB [auth C],
Q [auth A],
QA [auth B],
QB [auth C],
QC [auth D],
R [auth A],
RB [auth C],
S [auth A],
SA [auth B],
SB [auth C],
SC [auth D],
T [auth A],
TA [auth B],
TB [auth C],
TC [auth D],
UA [auth B],
UB [auth C],
UC [auth D],
V [auth A],
VA [auth B],
VB [auth C],
VC [auth D],
W [auth A],
WA [auth B],
WB [auth C],
WC [auth D],
XA [auth B],
XB [auth C],
XC [auth D],
Y [auth A],
YB [auth C],
YC [auth D],
Z [auth A],
ZA [auth B],
ZB [auth C],
ZC [auth D]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free:  0.258 (Depositor), 0.260 (DCC) 
  • R-Value Work:  0.209 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.212 (Depositor) 
Space Group: I 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.93α = 90
b = 131.05β = 99.3
c = 215.518γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2021-07-14
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Data collection, Database references, Refinement description
  • Version 1.2: 2025-09-17
    Changes: Database references, Structure summary