5IXY

Lactate Dehydrogenase in complex with hydroxylactam inhibitor compound 31: (2~{S})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one

• PDB DOI: https://doi.org/10.2210/pdb5IXY/pdb

• Classification: OXIREDUCTASE/OXIREDUCTASE INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2016-03-23 Released: 2016-09-14 
• Deposition Author(s): Chen, Z., Eigenbrot, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.279 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 

Starting Model: experimental

Literature

Cell Active Hydroxylactam Inhibitors of Human Lactate Dehydrogenase with Oral Bioavailability in Mice.

Purkey, H.E., Robarge, K., Chen, J., Chen, Z., Corson, L.B., Ding, C.Z., DiPasquale, A.G., Dragovich, P.S., Eigenbrot, C., Evangelista, M., Fauber, B.P., Gao, Z., Ge, H., Hitz, A., Ho, Q., Labadie, S.S., Lai, K.W., Liu, W., Liu, Y., Li, C., Ma, S., Malek, S., O'Brien, T., Pang, J., Peterson, D., Salphati, L., Sideris, S., Ultsch, M., Wei, B., Yen, I., Yue, Q., Zhang, H., Zhou, A.

(2016) ACS Med Chem Lett 7: 896-901

• PubMed: 27774125 
• DOI: https://doi.org/10.1021/acsmedchemlett.6b00190
• Primary Citation of Related Structures:  
  5IXS, 5IXY


• PubMed Abstract: 
  

  A series of trisubstituted hydroxylactams was identified as potent enzymatic and cellular inhibitors of human lactate dehydrogenase A. Utilizing structure-based design and physical property optimization, multiple inhibitors were discovered with <10 μM lactate IC ₅₀ in a MiaPaca2 cell line. Optimization of the series led to 29 , a potent cell active molecule (MiaPaca2 IC ₅₀ = 0.67 μM) that also possessed good exposure when dosed orally to mice.

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Organizational Affiliation: 

Genentech, Inc. , 1 DNA Way, South San Francisco, California 94080, United States.

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)

Macromolecule Content

• Total Structure Weight: 151.74 kDa 
• Atom Count: 10,593 
• Modelled Residue Count: 1,321 
• Deposited Residue Count: 1,324 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-lactate dehydrogenase A chain	A, B, C, D	331	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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAD	E [auth A], I [auth B], N [auth C], R [auth D]	NICOTINAMIDE-ADENINE-DINUCLEOTIDE C21 H27 N7 O14 P2 BAWFJGJZGIEFAR-NNYOXOHSSA-N
GN2	H [auth A], M [auth B], Q [auth C], S [auth D]	(2~{S})-5-(2-chlorophenyl)sulfanyl-2-(4-morpholin-4-ylphenyl)-4-oxidanyl-2-thiophen-3-yl-1,3-dihydropyridin-6-one C25 H23 Cl N2 O3 S2 SUFXXEIVBZJOAP-VWLOTQADSA-N
SO4	F [auth A], G [auth A], J [auth B], K [auth B], L [auth B], O [auth C], P [auth C]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.279 
• R-Value Work: 0.236 
• R-Value Observed: 0.237 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 78.452	α = 90
b = 80.696	β = 97.9
c = 102.236	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-09-14 
Deposition Author(s): Chen, Z., Eigenbrot, C.

Revision History  

• Version 1.0: 2016-09-14
  Type: Initial release
  
• Version 1.1: 2016-11-09
  Changes: Database references
• Version 1.2: 2023-09-27
  Changes: Data collection, Database references, Derived calculations, Refinement description