3CLD

Ligand binding domain of the glucocorticoid receptor complexed with fluticazone furoate

• PDB DOI: https://doi.org/10.2210/pdb3CLD/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-03-18 Released: 2008-06-24 
• Deposition Author(s): Shewchuk, L.M., McLay, I., Stewart, E., Biggadike, K.B., Hassell, A.M., Bledsoe, R.K.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.267 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 

Starting Model: experimental

Literature

X-ray crystal structure of the novel enhanced-affinity glucocorticoid agonist fluticasone furoate in the glucocorticoid receptor-ligand binding domain.

Biggadike, K., Bledsoe, R.K., Hassell, A.M., Kirk, B.E., McLay, I.M., Shewchuk, L.M., Stewart, E.L.

(2008) J Med Chem 51: 3349-3352

• PubMed: 18522385 
• DOI: https://doi.org/10.1021/jm800279t
• Primary Citation of Related Structures:  
  3CLD


• PubMed Abstract: 
  

  An X-ray crystal structure is reported for the novel enhanced-affinity glucocorticoid agonist fluticasone furoate (FF) in the ligand binding domain of the glucocorticoid receptor. Comparison of this structure with those of dexamethasone and fluticasone propionate shows the 17 alpha furoate ester to occupy more fully the lipophilic 17 alpha pocket on the receptor, which may account for the enhanced glucocorticoid receptor binding of FF.

---

Organizational Affiliation: 

[e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Hetero 4-mer - A2B2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 4-mer - A2B1C1 

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

Macromolecule Content

• Total Structure Weight: 64.01 kDa 
• Atom Count: 4,096 
• Modelled Residue Count: 502 
• Deposited Residue Count: 542 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucocorticoid receptor	A, C [auth B]	259	Homo sapiens	Mutation(s): 2  Gene Names: NR3C1, GRL
UniProt & NIH Common Fund Data Resources
Find proteins for P04150 (Homo sapiens) Explore P04150  Go to UniProtKB:  P04150
PHAROS:  P04150 GTEx:  ENSG00000113580

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Tif2 coactivator motif	B [auth H], D [auth C]	12	N/A	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15596 (Homo sapiens) Explore Q15596  Go to UniProtKB:  Q15596
PHAROS:  Q15596 GTEx:  ENSG00000140396

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GW6	E [auth A], F [auth B]	(6alpha,11alpha,14beta,16alpha,17alpha)-6,9-difluoro-17-{[(fluoromethyl)sulfanyl]carbonyl}-11-hydroxy-16-methyl-3-oxoan drosta-1,4-dien-17-yl furan-2-carboxylate C27 H29 F3 O6 S XTULMSXFIHGYFS-VLSRWLAYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GW6	BindingDB:  3CLD	Ki: 0.51 (nM) from 1 assay(s)
		IC50: min: 0.04, max: 0.8 (nM) from 2 assay(s)
		EC50: min: 0.4, max: 0.49 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.84 Å
• R-Value Free: 0.267 
• R-Value Work: 0.207 
• R-Value Observed: 0.210 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 127.34	α = 90
b = 127.34	β = 90
c = 77.772	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-06-24 
Deposition Author(s): Shewchuk, L.M., McLay, I., Stewart, E., Biggadike, K.B., Hassell, A.M., Bledsoe, R.K.

Revision History  

• Version 1.0: 2008-06-24
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2021-10-20
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2023-08-30
  Changes: Data collection, Refinement description