5ZXI | pdb_00005zxi

Co-crystal structure of an Inhibitor in complex with human PPARdelta LBD

• PDB DOI: https://doi.org/10.2210/pdb5ZXI/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli K-12
• Mutation(s): No 


• Deposited: 2018-05-21 Released: 2019-04-03 
• Deposition Author(s): Rani, S.T., Laxminarasimhan, A., Senaiar, R.S., Krishnamurthy, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 
  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work: 
  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.220 (Depositor) 

Literature

Selective PPAR delta Modulators Improve Mitochondrial Function: Potential Treatment for Duchenne Muscular Dystrophy (DMD).

Lagu, B., Kluge, A.F., Tozzo, E., Fredenburg, R., Bell, E.L., Goddeeris, M.M., Dwyer, P., Basinski, A., Senaiar, R.S., Jaleel, M., Tiwari, N.K., Panigrahi, S.K., Krishnamurthy, N.R., Takahashi, T., Patane, M.A.

(2018) ACS Med Chem Lett 9: 935-940

• PubMed: 30258544 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00287
• Primary Citation of Related Structures:  
  5ZXI


• PubMed Abstract: 
  

  The X-ray structure of the previously reported PPARδ modulator 1 bound to the ligand binding domain (LBD) revealed that the amide moiety in 1 exists in the thermodynamically disfavored cis -amide orientation. Isosteric replacement of the cis -amide with five-membered heterocycles led to the identification of imidazole 17 (MA-0204), a potent, selective PPARδ modulator with good pharmacokinetic properties. MA-0204 was tested in vivo in mice and in vitro in patient-derived muscle myoblasts (from Duchenne Muscular Dystrophy (DMD) patients); 17 altered the expression of PPARδ target genes and improved fatty acid oxidation, which supports the therapeutic hypothesis for the study of MA-0204 in DMD patients.

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Organizational Affiliation: 

Mitobridge, Inc. (a wholly owned subsidiary of Astellas Pharma.), 1030 Massachusetts Avenue, Cambridge, Massachusetts 02138, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: assay for oligomerization

Macromolecule Content

• Total Structure Weight: 63.75 kDa 
• Atom Count: 4,235 
• Modelled Residue Count: 496 
• Deposited Residue Count: 550 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor delta	A, B	275	Homo sapiens	Mutation(s): 0  Gene Names: PPARD, NR1C2, PPARB
UniProt & NIH Common Fund Data Resources
Find proteins for Q03181 (Homo sapiens) Explore Q03181  Go to UniProtKB:  Q03181
PHAROS:  Q03181 GTEx:  ENSG00000112033

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9LU (Subject of Investigation/LOI)	C [auth A], D [auth B]	6-[2-({2-[4-(furan-2-yl)phenyl]-5-methyl-1H-imidazol-1-yl}methyl)phenoxy]hexanoic acid C27 H28 N2 O4 PZVNGYWXLMIOJJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9LU	BindingDB:  5ZXI	EC50: 0.7 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free:  0.281 (Depositor), 0.280 (DCC) 
• R-Value Work:  0.217 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.220 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.795	α = 90
b = 76.644	β = 97.81
c = 96.663	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALEPACK	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2019-04-03 
Deposition Author(s): Rani, S.T., Laxminarasimhan, A., Senaiar, R.S., Krishnamurthy, N.

Revision History  

• Version 1.0: 2019-04-03
  Type: Initial release
  
• Version 1.1: 2024-03-27
  Changes: Data collection, Database references