7F80

Co-crystal structure of Inhibitor compound MA-211 in complex with human PPARdelta LBD

• PDB DOI: https://doi.org/10.2210/pdb7F80/pdb

• Classification: PROTEIN BINDING/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Escherichia phage EcSzw-2
• Mutation(s): No 


• Deposited: 2021-06-30 Released: 2022-07-06 
• 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: 2.80 Å
• R-Value Free: 0.300 
• R-Value Work: 0.204 
• R-Value Observed: 0.209 

Starting Model: experimental

Literature

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

Lakshminarasimhan, A., Rani, S.T., Senaiar, R.S., Krishnamurthy, N.

To be published.

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: 63.78 kDa 
• Atom Count: 4,176 
• Modelled Residue Count: 509 
• 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
1KF (Subject of Investigation/LOI)	C [auth A], D [auth B]	(3R)-3-methyl-6-[2-[[5-methyl-2-[4-(trifluoromethyl)phenyl]imidazol-1-yl]methyl]phenoxy]hexanoic acid C25 H27 F3 N2 O3 FMOPHFSPINWSOV-QGZVFWFLSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
1KF	BindingDB:  7F80	EC50: 0.1 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 0.300 
• R-Value Work: 0.204 
• R-Value Observed: 0.209 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 39.687	α = 90
b = 74.991	β = 97.89
c = 96.341	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
CrystalClear	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2022-07-06 
Deposition Author(s): Lakshminarasimhan, A., Rani, S.T., Senaiar, R.S., Krishnamurthy, N.

Revision History  

• Version 1.0: 2022-07-06
  Type: Initial release
  
• Version 1.1: 2023-11-29
  Changes: Data collection, Refinement description