4DK7 | pdb_00004dk7

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

PDB DOI: https://doi.org/10.2210/pdb4DK7/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., Xu, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free:
0.270 (Depositor), 0.265 (DCC)
R-Value Work:
0.230 (Depositor), 0.222 (DCC)
R-Value Observed:
0.276 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 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

PubMed: 22406115 Search on PubMed
DOI: https://doi.org/10.1016/j.bmcl.2012.02.028
Primary Citation 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.

Organizational Affiliation

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

Macromolecule Content

Total Structure Weight: 61.85 kDa
Atom Count: 4,178
Modeled Residue Count: 488
Deposited Residue Count: 518
Unique protein chains: 2

Macromolecules

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| 3D Structure

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 Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P55055
Sequence Annotations Expand
Reference Sequence

Find similar proteins by: Sequence | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q15788
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0KS Query on 0KS Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth C] MOL2 format, chain E [auth A] MOL2 format, chain L [auth C] mmCIF format, chain E [auth A] mmCIF format, chain L [auth C]	E [auth A], L [auth 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		Interactions Focus chain E [auth A] Focus chain L [auth C] Interactions & Density Focus chain E [auth A] Focus chain L [auth C]
ACT Query on ACT Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	G [auth A] H [auth A] I [auth A] J [auth A] K [auth A] G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], M [auth C], N [auth C]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth C] Focus chain N [auth C]

Modified Residues 1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE Query on MSE	A, C	L-PEPTIDE LINKING	C₅ H₁₁ N O₂ Se		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
0KS	BindingDB: 4DK7	IC50: 20 (nM) from 1 assay(s)
0KS	BindingDB: 4DK7	EC50: 2930 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.45 Å
R-Value Free: 0.270 (Depositor), 0.265 (DCC)
R-Value Work: 0.230 (Depositor), 0.222 (DCC)
R-Value Observed: 0.276 (Depositor)

Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.261	α = 90
b = 87.261	β = 90
c = 197.709	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2012-03-21

Deposition Author(s):

Piper, D.E.

Xu, H.

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
Version 1.2: 2024-10-30
Changes: Data collection, Database references, Derived calculations, Structure summary