4DK7

Crystal structure of LXR ligand binding domain in complex with full agonist 1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.230 

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:  

  • 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 o ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Oxysterols receptor LXR-beta
A, C
247Homo sapiensMutation(s): 0 
Gene Names: NR1H2 (LXRB, NER, UNR)
Find proteins for P55055 (Homo sapiens)
Go to Gene View: NR1H2
Go to UniProtKB:  P55055
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nuclear receptor coactivator 1
B, D
12Homo sapiensMutation(s): 0 
Gene Names: NCOA1 (BHLHE74, SRC1)
EC: 2.3.1.48
Find proteins for Q15788 (Homo sapiens)
Go to Gene View: NCOA1
Go to UniProtKB:  Q15788
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ACT
Query on ACT

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Download CCD File 
A
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
CA
Query on CA

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Download CCD File 
A, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
0KS
Query on 0KS

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Download CCD File 
A, C
N-[4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl]-N-methylbenzenesulfonamide
C16 H13 F6 N O3 S
CNVKZYLQZYULJV-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MSE
Query on MSE
A, C
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
0KSIC50: 20 nM (98) BINDINGDB
0KSIC50: 20 nM BINDINGMOAD
0KSIC50: 20 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.45 Å
  • R-Value Free: 0.270 
  • R-Value Work: 0.230 
  • Space Group: P 43 21 2
Unit Cell:
Length (Å)Angle (°)
a = 87.261α = 90.00
b = 87.261β = 90.00
c = 197.709γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
PDB_EXTRACTdata extraction
DENZOdata reduction
CNSphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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

Revision History 

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