1KNU | pdb_00001knu

LIGAND BINDING DOMAIN OF THE HUMAN PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA IN COMPLEX WITH A SYNTHETIC AGONIST

• PDB DOI: https://doi.org/10.2210/pdb1KNU/pdb

• Classification: DNA BINDING PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2001-12-19 Released: 2002-12-19 
• Deposition Author(s): Svensson, L.A., Mortensen, S.B., Fleckner, J., Woeldike, H.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.264 (Depositor) 
• R-Value Work: 
  0.224 (Depositor) 

Starting Model: experimental

Literature

Novel tricyclic-alpha-alkyloxyphenylpropionic acids: dual PPARalpha/gamma agonists with hypolipidemic and antidiabetic activity

Sauerberg, P., Pettersson, I., Jeppesen, L., Bury, P.S., Mogensen, J.P., Wassermann, K., Brand, C.L., Sturis, J., Woldike, H.F., Fleckner, J., Andersen, A.-S.T., Mortensen, S.B., Svensson, L.A., Rasmussen, H.B., Lehmann, S.V., Polivka, Z., Sindelar, K., Panajotova, V., Ynddal, L., Wulff, E.M.

(2002) J Med Chem 45: 789-804

• PubMed: 11831892 
• DOI: https://doi.org/10.1021/jm010964g
• Primary Citation Related Structures: 
  1KNU


• PubMed Abstract: 
  

  Synthesis and structure-activity relationships of tricyclic alpha-ethoxy-phenylpropionic acid derivatives guided by in vitro PPARalpha and PPARgamma transactivation data and computer modeling led to the identification of the novel carbazole analogue, 3q, with dual PPARalpha (EC(50) = 0.36 microM) and PPARgamma (EC(50) = 0.17 microM) activity in vitro. Ten days treatment of db/db mice with 3q improved the insulin sensitivity, as measured by OGTT, better than that seen with both pioglitazone and rosiglitazone treatment, suggesting in vivo PPARgamma activity. Likewise, 3q lowered plasma triglycerides and cholesterol in high cholesterol fed rats after 4 days treatment, indicating in vivo PPARalpha activity. Investigations of the pharmacokinetics of selected compounds suggested that extended drug exposure improved the in vivo activity of in vitro active compounds.

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Organizational Affiliation: 
• Novo Nordisk A/S, Novo Nordisk Park E9 2.02, 2760 Måløv, Denmark. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 63.05 kDa 
• Atom Count: 4,303 
• Modeled Residue Count: 523 
• Deposited Residue Count: 548 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PEROXISOME PROLIFERATOR ACTIVATED RECEPTOR GAMMA	A, B	274	Homo sapiens	Mutation(s): 0  Gene Names: PPARG, NR1C3
UniProt & NIH Common Fund Data Resources
Find proteins for P37231 (Homo sapiens) Explore P37231  Go to UniProtKB:  P37231
PHAROS:  P37231 GTEx:  ENSG00000132170

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YPA	C [auth A]	(S)-3-(4-(2-CARBAZOL-9-YL-ETHOXY)-PHENYL)-2-ETHOXY-PROPIONIC ACID C25 H25 N O4 WUZIMDSVRIBNNI-DEOSSOPVSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.264 (Depositor) 
• R-Value Work:  0.224 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.27	α = 90
b = 63.44	β = 101.84
c = 119.24	γ = 90

Software Package:

Software Name	Purpose
XDS	data scaling
XDS	data reduction
CNX	refinement
CNX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2002-12-19 
Deposition Author(s): Svensson, L.A., Mortensen, S.B., Fleckner, J., Woeldike, H.F.

Revision History  

• Version 1.0: 2002-12-19
  Type: Initial release
  
• Version 1.1: 2008-04-27
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Data collection, Refinement description
• Version 1.4: 2023-10-25
  Changes: Data collection, Database references, Derived calculations, Refinement description