5XMX

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

• PDB DOI: https://doi.org/10.2210/pdb5XMX/pdb

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


• Deposited: 2017-05-16 Released: 2018-05-23 
• Deposition Author(s): Lakshminarasimhan, A., Rani, S.T., Senaiar, R.S., Krishnamurthy, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 

Starting Model: experimental

Literature

Novel highly selective peroxisome proliferator-activated receptor delta (PPAR delta) modulators with pharmacokinetic properties suitable for once-daily oral dosing.

Lagu, B., Kluge, A.F., Fredenburg, R.A., Tozzo, E., Senaiar, R.S., Jaleel, M., Panigrahi, S.K., Tiwari, N.K., Krishnamurthy, N.R., Takahashi, T., Patane, M.A.

(2017) Bioorg Med Chem Lett 27: 5230-5234

• PubMed: 29103972 
• DOI: https://doi.org/10.1016/j.bmcl.2017.10.037
• Primary Citation of Related Structures:  
  5XMX


• PubMed Abstract: 
  

  Optimization of benzamide PPARδ modulator 1 led to (E)-6-(2-((4-(furan-2-yl)-N-methylbenzamido)methyl)phenoxy)-4-methylhex-4-enoic acid (18), a potent selective PPARδ modulator with significantly improved exposure in multiple species following oral administration.

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Organizational Affiliation: 

Mitobridge, Inc., 1030 Massachusetts Ave., Cambridge, MA 02138, United States. Electronic address: [e-mail].

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 63.73 kDa 
• Atom Count: 4,335 
• Modelled Residue Count: 502 
• 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
89L	C [auth A], D [auth B]	(E)-6-[2-[[[4-(furan-2-yl)phenyl]carbonyl-methyl-amino]methyl]phenoxy]-4-methyl-hex-4-enoic acid C26 H27 N O5 WZFMWAHUFRLQRH-XDJHFCHBSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
89L	BindingDB:  5XMX	Kd: 57 (nM) from 1 assay(s)
		EC50: min: 5, max: 270 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.282 
• R-Value Work: 0.212 
• R-Value Observed: 0.215 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.84	α = 90
b = 76.39	β = 97.74
c = 96.73	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data processing
XDS	data reduction
XDS	data scaling
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-05-23 
Deposition Author(s): Lakshminarasimhan, A., Rani, S.T., Senaiar, R.S., Krishnamurthy, N.

Revision History  

• Version 1.0: 2018-05-23
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Refinement description