6TDC | pdb_00006tdc

PPAR gamma ligand binding domain in complex with MRL-871

• PDB DOI: https://doi.org/10.2210/pdb6TDC/pdb

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


• Deposited: 2019-11-08 Released: 2020-11-18 
• Deposition Author(s): de Vries, R.M.J.M., Leijten-van de Gevel, I.A., van Herk, K.H.N., Brunsveld, L.
• Funding Organization(s): Netherlands Organisation for Scientific Research

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free: 
  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Starting Model: experimental

Literature

Binding of PPAR(gamma) to MRL871

Leijten-van de Gevel, I.A., van Herk, K.H.N., de Vries, R.M.J.M., Brunsveld, L.

To be published.

Biological Assembly 1  

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

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

Biological Assembly Evidence: native gel electrophoresis

Macromolecule Content 

• Total Structure Weight: 33.84 kDa 
• Atom Count: 2,155 
• Modeled Residue Count: 260 
• Deposited Residue Count: 292 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peroxisome proliferator-activated receptor gamma	A	292	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4F1 (Subject of Investigation/LOI)	B [auth A]	4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-1H-indazol-3-yl}benzoic acid C22 H12 Cl F3 N2 O3 DANLZOIRUUHIIX-UHFFFAOYSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
4F1	BindingDB:  6TDC	Ki: min: 160, max: 230 (nM) from 3 assay(s)
		Kd: 250 (nM) from 1 assay(s)
		IC50: min: 130, max: 7200 (nM) from 3 assay(s)
		EC50: min: 170, max: 9100 (nM) from 5 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.33 Å
• R-Value Free:  0.239 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.142	α = 90
b = 93.142	β = 90
c = 130.574	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
PDB_EXTRACT	data extraction
DIALS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-11-18 
Deposition Author(s): de Vries, R.M.J.M., Leijten-van de Gevel, I.A., van Herk, K.H.N., Brunsveld, L.

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Funding Organization	Location	Grant Number
Netherlands Organisation for Scientific Research	Netherlands	024.001.035

Revision History  

• Version 1.0: 2020-11-18
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Refinement description