2Q5G | pdb_00002q5g

Ligand binding domain of PPAR delta receptor in complex with a partial agonist

• PDB DOI: https://doi.org/10.2210/pdb2Q5G/pdb

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


• Deposited: 2007-06-01 Released: 2008-06-03 
• Deposition Author(s): Pettersson, I., Sauerberg, P., Johansson, E., Hoffman, I., Tari, L.W., Hunter, M.J., Nix, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free: 
  0.305 (Depositor), 0.302 (DCC) 
• R-Value Work: 
  0.225 (Depositor), 0.231 (DCC) 
• R-Value Observed: 
  0.229 (Depositor) 

Starting Model: experimental

Literature

Design of a partial PPARdelta agonist.

Pettersson, I., Ebdrup, S., Havranek, M., Pihera, P., Korinek, M., Mogensen, J.P., Jeppesen, C.B., Johansson, E., Sauerberg, P.

(2007) Bioorg Med Chem Lett 17: 4625-4629

• PubMed: 17560785 
• DOI: https://doi.org/10.1016/j.bmcl.2007.05.079
• Primary Citation Related Structures: 
  2Q5G


• PubMed Abstract: 
  

  Structure based ligand design was used in order to design a partial agonist for the PPARdelta receptor. The maximum activation in the transactivation assay was reduced from 87% to 39%. The crystal structure of the ligand binding domain of the PPARdelta receptor in complex with compound 2 was determined in order to understand the structural changes which gave rise to the decrease in maximum activation.

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Organizational Affiliation: 
• Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark. [e-mail]

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors and generated by PQS (software)

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 66.17 kDa 
• Atom Count: 3,876 
• Modeled Residue Count: 479 
• Deposited Residue Count: 566 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor delta	A, B	283	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
1FA	C [auth A], D [auth B]	[(7-{[2-(3-MORPHOLIN-4-YLPROP-1-YN-1-YL)-6-{[4-(TRIFLUOROMETHYL)PHENYL]ETHYNYL}PYRIDIN-4-YL]THIO}-2,3-DIHYDRO-1H-INDEN- 4-YL)OXY]ACETIC ACID C32 H27 F3 N2 O4 S AKQAEZPFLKFQCZ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1FA	BindingDB:  2Q5G	EC50: 130 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.70 Å
• R-Value Free:  0.305 (Depositor), 0.302 (DCC) 
• R-Value Work:  0.225 (Depositor), 0.231 (DCC) 
• R-Value Observed: 0.229 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 112.577	α = 90
b = 65.603	β = 124.05
c = 101.149	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	data reduction
PHASES	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-03 
Deposition Author(s): Pettersson, I., Sauerberg, P., Johansson, E., Hoffman, I., Tari, L.W., Hunter, M.J., Nix, J.

Revision History  

• Version 1.0: 2008-06-03
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.2: 2018-01-24
  Changes: Structure summary
• Version 1.3: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary