4DK8 | pdb_00004dk8

Crystal structure of LXR ligand binding domain in complex with partial agonist 5

• PDB DOI: https://doi.org/10.2210/pdb4DK8/pdb

• Classification: TRANSCRIPTION/Peptide/Agonist
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-02-03 Released: 2012-03-21 
• Deposition Author(s): Piper, D.E., Kopecky, D.J., Xu, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free: 
  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work: 
  0.245 (Depositor), 0.230 (DCC) 
• R-Value Observed: 
  0.312 (Depositor) 

Literature

Discovery of a new binding mode for a series of liver X receptor agonists.

Kopecky, D.J., Jiao, X.Y., Fisher, B., McKendry, S., Labelle, M., Piper, D.E., Coward, P., Shiau, A.K., Escaron, P., Danao, J., Chai, A., Jaen, J., Kayser, F.

(2012) Bioorg Med Chem Lett 22: 2407-2410

• PubMed: 22406115 
• DOI: https://doi.org/10.1016/j.bmcl.2012.02.028
• Primary Citation of Related Structures:  
  4DK7, 4DK8


• PubMed Abstract: 
  

  Structural modification of a series of dual LXRα/β agonists led to the identification of a new class of LXRβ partial agonists. An X-ray co-crystal structure shows that a representative member of this series, pyrrole 5, binds to LXRβ with a reversed orientation compared to 1.

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Organizational Affiliation: 

Department of Medicinal Chemistry, Amgen Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA. [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: 61.36 kDa 
• Atom Count: 4,081 
• Modelled Residue Count: 486 
• Deposited Residue Count: 518 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Oxysterols receptor LXR-beta	A, C	247	Homo sapiens	Mutation(s): 0  Gene Names: NR1H2, LXRB, NER, UNR
UniProt & NIH Common Fund Data Resources
Find proteins for P55055 (Homo sapiens) Explore P55055  Go to UniProtKB:  P55055
PHAROS:  P55055 GTEx:  ENSG00000131408

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Nuclear receptor coactivator 1	B, D	12	Homo sapiens	Mutation(s): 0  EC: 2.3.1.48
UniProt & NIH Common Fund Data Resources
Find proteins for Q15788 (Homo sapiens) Explore Q15788  Go to UniProtKB:  Q15788
PHAROS:  Q15788 GTEx:  ENSG00000084676

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0KT	E [auth A], K [auth C]	N-methyl-N-(4-{(1S)-2,2,2-trifluoro-1-hydroxy-1-[1-(2-methoxyethyl)-1H-pyrrol-2-yl]ethyl}phenyl)benzenesulfonamide C22 H23 F3 N2 O4 S YNUCWQDMZHYFEC-NRFANRHFSA-N
ACT	F [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	G [auth A], H [auth A], I [auth A], J [auth A], L [auth C], M [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
0KT	BindingDB:  4DK8	IC50: 1800 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.75 Å
• R-Value Free:  0.278 (Depositor), 0.270 (DCC) 
• R-Value Work:  0.245 (Depositor), 0.230 (DCC) 
• R-Value Observed: 0.312 (Depositor) 

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 88.145	α = 90
b = 88.145	β = 90
c = 198.45	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-03-21 
Deposition Author(s): Piper, D.E., Kopecky, D.J., Xu, H.

Revision History  

• Version 1.0: 2012-03-21
  Type: Initial release
  
• Version 1.1: 2012-05-09
  Changes: Database references
• Version 1.2: 2024-02-28
  Changes: Data collection, Database references, Derived calculations