2Q5G

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.305
R-Value Work: 0.225
R-Value Observed: 0.229

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

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 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2007.05.079
Primary Citation of 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.

Organizational Affiliation

Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark. inpe@novonordisk.com

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q03181
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1FA Query on 1FA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	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		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

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
R-Value Work: 0.225
R-Value Observed: 0.229
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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-06-03

Deposition Author(s):

Revision History (Full details and data files)

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