Biological Assembly 1  

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

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

Macromolecule Content

• Total Structure Weight: 153.05 kDa 
• Atom Count: 10,715 
• Modelled Residue Count: 1,318 
• Deposited Residue Count: 1,348 
• Unique protein chains: 1

 4AJP

Human LDHA in complex with 2-((4-(4-((3-((2-methyl-1,3-benzothiazol- 6yl)amino)-3-oxo-propyl)amino)-4-oxo-butyl)phenyl)methyl)propanedioic acid

• PDB DOI:  https://doi.org/10.2210/pdb4AJP/pdb

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


• Deposited: 2012-02-16 Released: 2012-03-21 
• Deposition Author(s): Tucker, J.A., Brassington, C., Caputo, A., Ward, R., Pearson, S., Watson, M., Tart, J., Davies, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.215 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 

Literature

The Design and Synthesis of Novel Lactate Dehydrogenase a Inhibitors by Fragment-Based Lead Generation

Ward, R., Brassington, C., Breeze, A.L., Caputo, A., Critchlow, S., Davies, G., Goodwin, L., Hassall, G., Greenwood, R., Holdgate, G., Mrosek, M., Norman, R.A., Pearson, S., Tart, J., Tucker, J.A., Vogtherr, M., Whittaker, D., Wingfield, J., Winter, J., Hudson, K.

(2012) J Med Chem 55: 3285

• PubMed: 22417091 
• DOI: https://doi.org/10.1021/jm201734r
• Primary Citation of Related Structures:  
  4AJ1, 4AJ2, 4AJ4, 4AJE, 4AJH, 4AJI, 4AJJ, 4AJK, 4AJL, 4AJN, 4AJO, 4AJP, 4AL4


• PubMed Abstract: 
  

Lactate dehydrogenase A (LDHA) catalyzes the conversion of pyruvate to lactate, utilizing NADH as a cofactor. It has been identified as a potential therapeutic target in the area of cancer metabolism. In this manuscript we report our progress using fragment-based lead generation (FBLG), assisted by X-ray crystallography to develop small molecule LDHA inhibitors. Fragment hits were identified through NMR and SPR screening and optimized into lead compounds with nanomolar binding affinities via fragment linking. Also reported is their modification into cellular active compounds suitable for target validation work.

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Organizational Affiliation: 

Oncology and Discovery Sciences iMEDs, AstraZeneca, Mereside, Alderley Park, Macclesfield, Cheshire, SK10 4TG, UK. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
L-LACTATE DEHYDROGENASE A CHAIN	A, B, C, D	337	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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
88N	E [auth A], K [auth B], Q [auth C], T [auth D]	{4-[4-({3-[(2-METHYL-1,3-BENZOTHIAZOL-6-YL)AMINO]-3-OXOPROPYL}AMINO)-4-OXOBUTYL]BENZYL}PROPANEDIOIC ACID C25 H27 N3 O6 S SGFJAJFBGVAOFW-UHFFFAOYSA-N
SO4	F [auth A], G [auth A], H [auth A], I [auth A], L [auth B], M [auth B], N [auth B], R [auth C], S [auth C], U [auth D], V [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	J [auth B], O [auth C], P [auth C]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
88N	Binding MOAD:  4AJP	Kd: 93 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.38 Å
• R-Value Free: 0.215 
• R-Value Work: 0.166 
• R-Value Observed: 0.168 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 63.98	α = 90
b = 136.78	β = 102.31
c = 83.79	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Tucker, J.A., Brassington, C., Caputo, A., Ward, R., Pearson, S., Watson, M., Tart, J., Davies, G.

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2012-04-25
  Changes: Other
• Version 1.2: 2014-09-17
  Changes: Atomic model, Derived calculations, Non-polymer description