4DK8

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.312 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


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

  • DOI: 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 ...

    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.


    Organizational Affiliation

    Department of Medicinal Chemistry, Amgen Inc., 1120 Veterans Blvd., South San Francisco, CA 94080, USA. dkopecky@amgen.com



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxysterols receptor LXR-betaA, C247Homo sapiensMutation(s): 0 
Gene Names: NR1H2LXRBNERUNR
Find proteins for P55055 (Homo sapiens)
Explore P55055 
Go to UniProtKB:  P55055
NIH Common Fund Data Resources
PHAROS:  P55055
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Nuclear receptor coactivator 1B, D12Homo sapiensMutation(s): 0 
Gene Names: NCOA1BHLHE74SRC1
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Explore Q15788 
Go to UniProtKB:  Q15788
NIH Common Fund Data Resources
PHAROS:  Q15788
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0KT
Query on 0KT

Download Ideal Coordinates CCD File 
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
 Ligand Interaction
ACT
Query on ACT

Download Ideal Coordinates CCD File 
F [auth A]ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

Download Ideal Coordinates CCD File 
G [auth A], H [auth A], I [auth A], J [auth A], L [auth C], M [auth C]CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0KTIC50:  1800   nM  BindingDB
ACTIC50 :  1800   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.75 Å
  • R-Value Free: 0.278 
  • R-Value Work: 0.245 
  • R-Value Observed: 0.312 
  • Space Group: P 43 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.145α = 90
b = 88.145β = 90
c = 198.45γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-03-21
    Type: Initial release
  • Version 1.1: 2012-05-09
    Changes: Database references