+Open data
-Basic information
Entry | Database: PDB / ID: 3fc6 | ||||||
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Title | hRXRalpha & mLXRalpha with an indole Pharmacophore, SB786875 | ||||||
Components |
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Keywords | TRANSCRIPTION / Liver X receptor / nuclear hormone receptors / agonists / epoxycholesterol / DNA-binding / Host-virus interaction / Metal-binding / Nucleus / Polymorphism / Receptor / Transcription regulation / Ubl conjugation / Zinc / Zinc-finger | ||||||
Function / homology | Function and homology information negative regulation of secretion of lysosomal enzymes / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / sterol response element binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / cellular lipid metabolic process / negative regulation of pancreatic juice secretion / phosphatidylcholine acyl-chain remodeling / positive regulation of cholesterol transport ...negative regulation of secretion of lysosomal enzymes / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / sterol response element binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / cellular lipid metabolic process / negative regulation of pancreatic juice secretion / phosphatidylcholine acyl-chain remodeling / positive regulation of cholesterol transport / negative regulation of response to endoplasmic reticulum stress / negative regulation of macrophage activation / negative regulation of pinocytosis / sterol homeostasis / VLDLR internalisation and degradation / positive regulation of toll-like receptor 4 signaling pathway / positive regulation of triglyceride biosynthetic process / positive regulation of transporter activity / retinoic acid-responsive element binding / NR1H2 & NR1H3 regulate gene expression linked to gluconeogenesis / NR1H2 & NR1H3 regulate gene expression linked to triglyceride lipolysis in adipose / NR1H2 & NR1H3 regulate gene expression to limit cholesterol uptake / positive regulation of thyroid hormone mediated signaling pathway / NR1H2 & NR1H3 regulate gene expression linked to lipogenesis / positive regulation of fatty acid biosynthetic process / negative regulation of lipid transport / triglyceride homeostasis / Carnitine metabolism / anatomical structure development / ion binding / Regulation of pyruvate dehydrogenase (PDH) complex / retinoic acid binding / positive regulation of vitamin D receptor signaling pathway / nuclear vitamin D receptor binding / apoptotic cell clearance / negative regulation of cold-induced thermogenesis / Signaling by Retinoic Acid / DNA binding domain binding / nuclear steroid receptor activity / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / LBD domain binding / negative regulation of cholesterol storage / lipid homeostasis / positive regulation of cholesterol efflux / Synthesis of bile acids and bile salts / retinoic acid receptor signaling pathway / positive regulation of lipid biosynthetic process / Endogenous sterols / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / positive regulation of bone mineralization / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / nuclear retinoid X receptor binding / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / response to retinoic acid / Recycling of bile acids and salts / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / positive regulation of protein metabolic process / Regulation of lipid metabolism by PPARalpha / hormone-mediated signaling pathway / cholesterol homeostasis / BMAL1:CLOCK,NPAS2 activates circadian gene expression / Activation of gene expression by SREBF (SREBP) / response to progesterone / transcription coregulator binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / peptide binding / negative regulation of proteolysis / SUMOylation of intracellular receptors / Heme signaling / mRNA transcription by RNA polymerase II / Transcriptional activation of mitochondrial biogenesis / lipid metabolic process / PPARA activates gene expression / Cytoprotection by HMOX1 / chromatin DNA binding / negative regulation of inflammatory response / Activation of anterior HOX genes in hindbrain development during early embryogenesis / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / Transcriptional regulation of granulopoiesis / RNA polymerase II transcription regulator complex / fatty acid biosynthetic process / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / cellular response to lipopolysaccharide / transcription regulator complex / sequence-specific DNA binding / cell differentiation / receptor complex / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of DNA-templated transcription / chromatin Similarity search - Function | ||||||
Biological species | Homo sapiens (human) Mus musculus (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.063 Å | ||||||
Authors | Washburn, D.G. / Hoang, T.H. / Campobasso, N. / Smallwood, A. / Parks, D.J. / Webb, C.L. / Frank, K. / Nord, M. / Duraiswami, C. / Evans, C. ...Washburn, D.G. / Hoang, T.H. / Campobasso, N. / Smallwood, A. / Parks, D.J. / Webb, C.L. / Frank, K. / Nord, M. / Duraiswami, C. / Evans, C. / Jaye, M. / Thompson, S.K. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Synthesis and SAR of potent LXR agonists containing an indole pharmacophore. Authors: Washburn, D.G. / Hoang, T.H. / Campobasso, N. / Smallwood, A. / Parks, D.J. / Webb, C.L. / Frank, K.A. / Nord, M. / Duraiswami, C. / Evans, C. / Jaye, M. / Thompson, S.K. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3fc6.cif.gz | 195.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3fc6.ent.gz | 154.6 KB | Display | PDB format |
PDBx/mmJSON format | 3fc6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fc/3fc6 ftp://data.pdbj.org/pub/pdb/validation_reports/fc/3fc6 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 27114.465 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P19793 #2: Protein | Mass: 30618.035 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse) / References: UniProt: Q91X41, UniProt: Q9Z0Y9*PLUS #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.25 Å3/Da / Density % sol: 45.22 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 23, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.06→44.2 Å / Num. all: 62907 / Num. obs: 58748 / % possible obs: 93.4 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Biso Wilson estimate: 26.1 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 7.9 |
Reflection shell | Resolution: 2.06→2.13 Å / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 2.2 / % possible all: 71.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.063→44.2 Å / SU ML: 0.34 / σ(F): 0.03 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.174 Å2 / ksol: 0.342 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.063→44.2 Å
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LS refinement shell |
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