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- PDB-5i4v: Discovery of novel, orally efficacious Liver X Receptor (LXR) bet... -

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Basic information

Entry
Database: PDB / ID: 5i4v
TitleDiscovery of novel, orally efficacious Liver X Receptor (LXR) beta agonists
Components
  • Oxysterols receptor LXR-beta,Nuclear receptor coactivator 2
  • Retinoic acid receptor RXR-beta,Nuclear receptor coactivator 2
KeywordsDNA BINDING PROTEIN / LXRbeta-LBD / RXRbeta-LBD / heterodimer / agonist
Function / homology
Function and homology information


positive regulation of secretion of lysosomal enzymes / positive regulation of high-density lipoprotein particle assembly / positive regulation of pancreatic juice secretion / phosphatidylcholine acyl-chain remodeling / negative regulation of response to endoplasmic reticulum stress / ventricular cardiac muscle cell differentiation / negative regulation of pinocytosis / maternal placenta development / regulation of lipid storage / positive regulation of triglyceride biosynthetic process ...positive regulation of secretion of lysosomal enzymes / positive regulation of high-density lipoprotein particle assembly / positive regulation of pancreatic juice secretion / phosphatidylcholine acyl-chain remodeling / negative regulation of response to endoplasmic reticulum stress / ventricular cardiac muscle cell differentiation / negative regulation of pinocytosis / maternal placenta development / regulation of lipid storage / positive regulation of triglyceride biosynthetic process / apolipoprotein A-I receptor binding / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / positive regulation of lipid storage / positive regulation of fatty acid biosynthetic process / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / negative regulation of lipid transport / positive regulation of vitamin D receptor signaling pathway / positive regulation of cholesterol transport / negative regulation of cold-induced thermogenesis / Signaling by Retinoic Acid / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / negative regulation of type II interferon-mediated signaling pathway / negative regulation of cholesterol storage / locomotor rhythm / aryl hydrocarbon receptor binding / nuclear steroid receptor activity / cellular response to Thyroglobulin triiodothyronine / negative regulation of macrophage derived foam cell differentiation / regulation of lipid metabolic process / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / cardiac muscle cell proliferation / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / positive regulation of bone mineralization / nuclear retinoid X receptor binding / retinoic acid receptor signaling pathway / cellular response to hormone stimulus / Recycling of bile acids and salts / transcription regulator inhibitor activity / VLDLR internalisation and degradation / intracellular receptor signaling pathway / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / hormone-mediated signaling pathway / positive regulation of adipose tissue development / cellular response to retinoic acid / : / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / negative regulation of proteolysis / regulation of cellular response to insulin stimulus / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / response to progesterone / Activation of gene expression by SREBF (SREBP) / cholesterol homeostasis / nuclear receptor binding / negative regulation of smoothened signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / response to nutrient levels / mRNA transcription by RNA polymerase II / circadian regulation of gene expression / chromatin DNA binding / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Cytoprotection by HMOX1 / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / negative regulation of inflammatory response / RNA polymerase II transcription regulator complex / nuclear receptor activity / : / sequence-specific double-stranded DNA binding / nervous system development / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / Estrogen-dependent gene expression / in utero embryonic development / cell differentiation / DNA-binding transcription factor activity, RNA polymerase II-specific / transcription coactivator activity / protein dimerization activity / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / protein domain specific binding / negative regulation of gene expression / negative regulation of DNA-templated transcription
Similarity search - Function
Liver X receptor / Retinoid X receptor/HNF4 / : / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 ...Liver X receptor / Retinoid X receptor/HNF4 / : / Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / : / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / Retinoid X Receptor / Retinoid X Receptor / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain / Nuclear hormone receptor-like domain superfamily / Ligand-binding domain of nuclear hormone receptor / Nuclear receptor (NR) ligand-binding (LBD) domain profile. / Ligand binding domain of hormone receptors / Zinc finger, NHR/GATA-type / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-67S / Retinoic acid receptor RXR-beta / Oxysterols receptor LXR-beta / Nuclear receptor coactivator 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.61 Å
AuthorsChen, G. / McKeever, B.M.
CitationJournal: J.Med.Chem. / Year: 2016
Title: Discovery of a Novel, Orally Efficacious Liver X Receptor (LXR) beta Agonist.
Authors: Zheng, Y. / Zhuang, L. / Fan, K.Y. / Tice, C.M. / Zhao, W. / Dong, C. / Lotesta, S.D. / Leftheris, K. / Lindblom, P.R. / Liu, Z. / Shimada, J. / Noto, P.B. / Meng, S. / Hardy, A. / Howard, L. ...Authors: Zheng, Y. / Zhuang, L. / Fan, K.Y. / Tice, C.M. / Zhao, W. / Dong, C. / Lotesta, S.D. / Leftheris, K. / Lindblom, P.R. / Liu, Z. / Shimada, J. / Noto, P.B. / Meng, S. / Hardy, A. / Howard, L. / Krosky, P. / Guo, J. / Lipinski, K. / Kandpal, G. / Bukhtiyarov, Y. / Zhao, Y. / Lala, D. / Van Orden, R. / Zhou, J. / Chen, G. / Wu, Z. / McKeever, B.M. / McGeehan, G.M. / Gregg, R.E. / Claremon, D.A. / Singh, S.B.
History
DepositionFeb 12, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list / struct_ncs_dom_lim
Item: _citation.journal_id_CSD / _database_2.pdbx_DOI ..._citation.journal_id_CSD / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Oxysterols receptor LXR-beta,Nuclear receptor coactivator 2
B: Retinoic acid receptor RXR-beta,Nuclear receptor coactivator 2
E: Oxysterols receptor LXR-beta,Nuclear receptor coactivator 2
F: Retinoic acid receptor RXR-beta,Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)118,3426
Polymers117,3644
Non-polymers9772
Water73941
1
A: Oxysterols receptor LXR-beta,Nuclear receptor coactivator 2
B: Retinoic acid receptor RXR-beta,Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1713
Polymers58,6822
Non-polymers4891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1800 Å2
ΔGint-9 kcal/mol
Surface area21930 Å2
MethodPISA
2
E: Oxysterols receptor LXR-beta,Nuclear receptor coactivator 2
F: Retinoic acid receptor RXR-beta,Nuclear receptor coactivator 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,1713
Polymers58,6822
Non-polymers4891
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1840 Å2
ΔGint-9 kcal/mol
Surface area21480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.637, 101.221, 143.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21E
12B
22F

NCS domain segments:

Component-ID: _ / Refine code: _

Dom-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11VALVALASPASPAA218 - 4778 - 267
21VALVALASPASPEC218 - 4778 - 267
12GLUGLUGLNGLNBB297 - 5435 - 251
22GLUGLUGLNGLNFD297 - 5435 - 251

NCS ensembles :
ID
1
2

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Components

#1: Protein Oxysterols receptor LXR-beta,Nuclear receptor coactivator 2 / Liver X receptor beta / Nuclear receptor NER / Nuclear receptor subfamily 1 group H member 2 / ...Liver X receptor beta / Nuclear receptor NER / Nuclear receptor subfamily 1 group H member 2 / Ubiquitously-expressed nuclear receptor / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 30567.936 Da / Num. of mol.: 2
Mutation: Q259A, R261G, D262S, R264S,Q259A, R261G, D262S, R264S,Q259A, R261G, D262S, R264S,Q259A, R261G, D262S, R264S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1H2, LXRB, NER, UNR, NCOA2, BHLHE75, SRC2, TIF2 / Plasmid: pET28a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P55055, UniProt: Q15596
#2: Protein Retinoic acid receptor RXR-beta,Nuclear receptor coactivator 2 / Nuclear receptor subfamily 2 group B member 2 / Retinoid X receptor beta / NCoA-2 / Class E basic ...Nuclear receptor subfamily 2 group B member 2 / Retinoid X receptor beta / NCoA-2 / Class E basic helix-loop-helix protein 75 / bHLHe75 / Transcriptional intermediary factor 2 / hTIF2


Mass: 28114.312 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RXRB, NR2B2, NCOA2, BHLHE75, SRC2, TIF2 / Plasmid: pET21a(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P28702, UniProt: Q15596
#3: Chemical ChemComp-67S / {2-[(2R)-4-[4-(hydroxymethyl)-3-(methylsulfonyl)phenyl]-2-(propan-2-yl)piperazin-1-yl]-4-(trifluoromethyl)pyrimidin-5-yl}methanol


Mass: 488.524 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27F3N4O4S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 41 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1uL of scLXRbeta-LBD/scRXRbeta-LBD @ 10 mg protein/ml in 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 5 mM DTT containing 1mM ligand and less than 2%(v/v) DMSO was mixed with 1uL of reservoir ...Details: 1uL of scLXRbeta-LBD/scRXRbeta-LBD @ 10 mg protein/ml in 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 5 mM DTT containing 1mM ligand and less than 2%(v/v) DMSO was mixed with 1uL of reservoir solution (0.2M LiCl, 16-20%(w/v) PEG3350, 7-10%(v/v) ethylene glycol, 0.01M Strontium chloride) on a circular, silanized glass cover slide and inverted and sealed with silicon grease over a well of 200uL of reservoir solution. Crystallization plates were incubated at 23 deg C for 2-5 days before rods would appear measuring 50 to 100um long.

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Data collection

DiffractionMean temperature: 100 K / Ambient temp details: CryoJet
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 1.075 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.075 Å / Relative weight: 1
ReflectionResolution: 2.609→82.67 Å / Num. obs: 29640 / % possible obs: 95.25 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / Biso Wilson estimate: 59.14 Å2 / Net I/σ(I): 13.3
Reflection shellResolution: 2.609→2.68 Å / Redundancy: 5.5 % / Mean I/σ(I) obs: 1.24 / % possible all: 71.3

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Processing

Software
NameVersionClassification
REFMAC5.8.0071refinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1UHL

1uhl


Resolution: 2.61→47.72 Å / Cor.coef. Fo:Fc: 0.944 / Cor.coef. Fo:Fc free: 0.924 / SU B: 33.343 / SU ML: 0.315 / Cross valid method: THROUGHOUT / ESU R Free: 0.349 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24815 1479 5 %RANDOM
Rwork0.20843 ---
obs0.2105 28161 95.27 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 47.114 Å2
Baniso -1Baniso -2Baniso -3
1-0.07 Å20 Å20 Å2
2--0.02 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.61→47.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7536 0 66 41 7643
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0197743
X-RAY DIFFRACTIONr_bond_other_d0.0030.027678
X-RAY DIFFRACTIONr_angle_refined_deg1.1331.98510459
X-RAY DIFFRACTIONr_angle_other_deg0.895317616
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5655926
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.83323.565359
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.768151419
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.621566
X-RAY DIFFRACTIONr_chiral_restr0.0570.21195
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0218533
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021775
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.9434.5153740
X-RAY DIFFRACTIONr_mcbond_other1.9444.5143739
X-RAY DIFFRACTIONr_mcangle_it3.1876.7554654
X-RAY DIFFRACTIONr_mcangle_other3.1866.7574655
X-RAY DIFFRACTIONr_scbond_it2.4884.894003
X-RAY DIFFRACTIONr_scbond_other2.4884.894003
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.2557.2035806
X-RAY DIFFRACTIONr_long_range_B_refined6.06135.5318785
X-RAY DIFFRACTIONr_long_range_B_other6.06135.5368786
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Weight position: 0.05

Ens-IDDom-IDAuth asym-IDNumberRms dev position (Å)
11A151530.11
12E151530.11
21B129700.12
22F129700.12
LS refinement shellResolution: 2.61→2.677 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 76 -
Rwork0.325 1533 -
obs--71.7 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.29520.10990.11821.3596-0.00270.3519-0.02640.00880.0393-0.06390.05450.07640.0097-0.0198-0.02820.0556-0.0075-0.0080.1121-0.0130.0173-6.1449-1.1094-22.3685
20.5649-0.1166-0.24141.17690.26782.0375-0.0468-0.09610.00970.07280.0048-0.08270.1530.26810.04190.01960.0409-0.00570.1253-0.01170.012112.8041-15.1235-5.8629
31.2021-0.2459-0.06190.33780.21670.92830.0788-0.0707-0.0873-0.0034-0.03910.01270.1224-0.0688-0.03960.0639-0.0378-0.01960.07550.00980.0101-15.16419.971612.9218
40.75220.0907-0.31571.40590.210.0258-0.11160.10340.05690.1079-0.01890.00120.097-0.13370.0107-0.01070.00470.0991-0.03740.0274-2.521428.992730.196
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A218 - 477
2X-RAY DIFFRACTION2B297 - 543
3X-RAY DIFFRACTION3E218 - 477
4X-RAY DIFFRACTION4F297 - 544

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