PDBsum entry 1osh

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Transcription PDB id
Protein chain
216 a.a. *
Waters ×179
* Residue conservation analysis
PDB id:
Name: Transcription
Title: A chemical, genetic, and structural analysis of the nuclear bile acid receptor fxr
Structure: Bile acid receptor. Chain: a. Fragment: ligand binding domain. Synonym: farnesoid x-activated receptor, farnesol receptor hrr-1, retinoid x receptor-interacting protein 14, rxr- interacting protein 14. Engineered: yes
Source: Homo sapiens. Human. Organism_taxid: 9606. Gene: nr1h4. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.
1.80Å     R-factor:   0.215     R-free:   0.234
Authors: M.Downes,M.A.Verdecia,A.J.Roecker,R.Hughes,J.B.Hogenesch, H.R.Kast-Woelbern,M.E.Bowman,J.-L.Ferrer,A.M.Anisfeld, P.A.Edwards,J.M.Rosenfeld,J.G.A.Alvarez,J.P.Noel, K.C.Nicolaou,R.M.Evans
Key ref:
M.Downes et al. (2003). A chemical, genetic, and structural analysis of the nuclear bile acid receptor FXR. Mol Cell, 11, 1079-1092. PubMed id: 12718892 DOI: 10.1016/S1097-2765(03)00104-7
19-Mar-03     Release date:   23-Sep-03    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q96RI1  (NR1H4_HUMAN) -  Bile acid receptor
486 a.a.
216 a.a.*
Key:    PfamA domain  PfamB domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     nucleus   1 term 
  Biological process     steroid hormone mediated signaling pathway   2 terms 
  Biochemical function     DNA binding     4 terms  


DOI no: 10.1016/S1097-2765(03)00104-7 Mol Cell 11:1079-1092 (2003)
PubMed id: 12718892  
A chemical, genetic, and structural analysis of the nuclear bile acid receptor FXR.
M.Downes, M.A.Verdecia, A.J.Roecker, R.Hughes, J.B.Hogenesch, H.R.Kast-Woelbern, M.E.Bowman, J.L.Ferrer, A.M.Anisfeld, P.A.Edwards, J.M.Rosenfeld, J.G.Alvarez, J.P.Noel, K.C.Nicolaou, R.M.Evans.
The farnesoid X receptor (FXR) functions as a bile acid (BA) sensor coordinating cholesterol metabolism, lipid homeostasis, and absorption of dietary fats and vitamins. However, BAs are poor reagents for characterizing FXR functions due to multiple receptor independent properties. Accordingly, using combinatorial chemistry we evolved a small molecule agonist termed fexaramine with 100-fold increased affinity relative to natural compounds. Gene-profiling experiments conducted in hepatocytes with FXR-specific fexaramine versus the primary BA chenodeoxycholic acid (CDCA) produced remarkably distinct genomic targets. Highly diffracting cocrystals (1.78 A) of fexaramine bound to the ligand binding domain of FXR revealed the agonist sequestered in a 726 A(3) hydrophobic cavity and suggest a mechanistic basis for the initial step in the BA signaling pathway. The discovery of fexaramine will allow us to unravel the FXR genetic network from the BA network and selectively manipulate components of the cholesterol pathway that may be useful in treating cholesterol-related human diseases.
  Selected figure(s)  
Figure 2.
Figure 2. Solid Phase Synthesis of a 94 Membered Focused Library of Biaryl and Stilbene CinnamatesReagents and conditions: (a) 2.0 equiv of 3, 1.0 equiv of Merrifield Resin (0.91 mmol/g), 2.0 equiv of Cs[2]CO[3], 0.5 equiv of TBAI, DMF, 55°C, 24 hr; (b) 20% TFA in CH[2]Cl[2], 25°C, 1 hr; (c) 10.0 equiv of 4-bromobenzaldehyde, 0.05 equiv of AcOH, THF:MeOH (2:1), 25°C, 1 hr; then, 8.0 equiv of NaCNBH[3], THF:MeOH (2:1), 25°C, 2 hr; (d) for R^1COCl: 30.0 equiv of R^1COCl, 40.0 equiv of Et[3]N, 1.0 equiv of 4-DMAP, CH[2]Cl[2], 25°C, 12 hr; for R^1NCO: 30.0 equiv of R^1NCO, 40.0 equiv of Et[3]N, 1.0 equiv of 4-DMAP, DMF, 65°C, 60 hr; (e) 8.0 equiv of styrene, 10.0 equiv of Et[3]N, 0.5 equiv of Pd[2](dba)[3], 1.5 equiv of P(o-tol)[3], DMF, 90°C, 48 hr; (f) 5.0 equiv of boronic acid, 3.0 equiv Cs[2]CO[3], 0.5 equiv of Pd(PPh[3])[4], DMF, 90°C, 24 hr; (g)10.0 equiv of NaOMe, Et[2]O:MeOH (10:1), 25°C, 20 min. AcOH, acetic acid; 4-DMAP, 4-dimethylaminopyridine; DMF, N,N-dimethylformamide; Et, ethyl; Me, methyl; Pd(PPh[3])[4], tetrakis(triphenylphosphine)palladium(0); Pd[2](dba)[3], tris(dibezylideneacetone)dipalladium(0); P(o-tol)[3], tri-o-tolylphosphine; TBAI, tetrabutylammonium iodide; TEA, triethylamine; TFA, trifluoroacetic acid; THF, tetrahydrofuran.
Figure 7.
Figure 7. Crystal Structure of FXR Bound to Fexaramine(A) Structure of hFXR-LBD. Residues 248 to 270 and 286 to 476 of hFXR-LBD in complex with the high-affinity agonist fexaramine. The α helices are shown in blue, and the ligand is shown in gold embedded in a transparent van der Waals surface. The structural elements are numbered according to the canonical structure for the LBD of nuclear receptors (NSB ref for canonical label).(B) Sequence alignment of FXR, VDR, SXR, and RXRα LBDs. The secondary structural elements of the hFXR-LBD are shown above the FXR sequence in blue and are labeled accordingly (see Figure 1A). Hydrophobic residues involved in binding fexaramine are highlighted in violet. Polar interactions are shown in blue and red.(C) Close-up of the first set of interactions with fexaramine. The hexyl group protrudes out into solution while making weak van der Waals contact with I339 and L344. The fexaramine carbonyl oxygen participates in two hydrogen bonding interactions (H298 and S336). The methyl ester aliphatic chain makes van der Waals contacts with Met294, Leu352, and I356. No charged interactions are seen in contact with the methyl ester moiety itself.(D) Close-up of the second set of interactions with fexaramine. The double benzyl rings make van der Waals contact with 15 residues. The majority of the ligand binding pocket is hydrophobic and partially aromatic in nature.(E) Close-up of a proposed model for complexation of CDCA by FXR-LBD. CDCA was modeled on the experimentally derived orientation of fexaramine. CDCA's two hydroxyl groups are pointed toward the side chains of Y365 and H451 to putatively participate in favorable hydrogen bonding. This positions the CDCA carboxyl group in the same orientation as the fexaramine hexyl group, suggesting that it protrudes from the protein or makes contacts with the insertion domain region. Notably, glycine and taurine bile acid conjugates could be accommodated in this orientation, which affords steric accommodation of the cognate tails.
  The above figures are reprinted by permission from Cell Press: Mol Cell (2003, 11, 1079-1092) copyright 2003.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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Genome-wide tissue-specific farnesoid X receptor binding in mouse liver and intestine.
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Identification of novel pathways that control farnesoid X receptor-mediated hypocholesterolemia.
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19242972 J.L.Boyer, and J.L.Boyer (2009).
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The major human pregnane X receptor (PXR) splice variant, PXR.2, exhibits significantly diminished ligand-activated transcriptional regulation.
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18651760 M.D.Krasowski, E.J.Reschly, and S.Ekins (2008).
Intrinsic disorder in nuclear hormone receptors.
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Target flexibility: an emerging consideration in drug discovery and design.
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18391212 S.M.Soisson, G.Parthasarathy, A.D.Adams, S.Sahoo, A.Sitlani, C.Sparrow, J.Cui, and J.W.Becker (2008).
Identification of a potent synthetic FXR agonist with an unexpected mode of binding and activation.
  Proc Natl Acad Sci U S A, 105, 5337-5342.
PDB code: 3bej
18668687 T.Frankenberg, T.Miloh, F.Y.Chen, M.Ananthanarayanan, A.Q.Sun, N.Balasubramaniyan, I.Arias, K.D.Setchell, F.J.Suchy, and B.L.Shneider (2008).
The membrane protein ATPase class I type 8B member 1 signals through protein kinase C zeta to activate the farnesoid X receptor.
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17959250 F.Gilardi, N.Mitro, C.Godio, E.Scotti, D.Caruso, M.Crestani, and E.De Fabiani (2007).
The pharmacological exploitation of cholesterol 7alpha-hydroxylase, the key enzyme in bile acid synthesis: from binding resins to chromatin remodelling to reduce plasma cholesterol.
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17601774 H.C.Shea, D.D.Head, K.D.Setchell, and D.W.Russell (2007).
Analysis of HSD3B7 knockout mice reveals that a 3alpha-hydroxyl stereochemistry is required for bile acid function.
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17545158 H.Lee, M.L.Hubbert, T.F.Osborne, K.Woodford, N.Zerangue, and P.A.Edwards (2007).
Regulation of the sodium/sulfate co-transporter by farnesoid X receptor alpha.
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17588816 S.Fiorucci, G.Rizzo, A.Donini, E.Distrutti, and L.Santucci (2007).
Targeting farnesoid X receptor for liver and metabolic disorders.
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Benefit of farnesoid X receptor inhibition in obstructive cholestasis.
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16908160 F.Y.Lee, H.Lee, M.L.Hubbert, P.A.Edwards, and Y.Zhang (2006).
FXR, a multipurpose nuclear receptor.
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16543221 J.C.Wang, N.Shah, C.Pantoja, S.H.Meijsing, J.D.Ho, T.S.Scanlan, and K.R.Yamamoto (2006).
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Farnesoid X receptor is essential for normal glucose homeostasis.
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16381851 R.B.Lanz, Z.Jericevic, W.J.Zuercher, C.Watkins, D.L.Steffen, R.Margolis, and N.J.McKenna (2006).
Nuclear Receptor Signaling Atlas ( hyperlinking the nuclear receptor signaling community.
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Endocrine functions of bile acids.
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FXR: a target for cholestatic syndromes?
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The X-ray structure of a hemipteran ecdysone receptor ligand-binding domain: comparison with a lepidopteran ecdysone receptor ligand-binding domain and implications for insecticide design.
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PDB code: 1z5x
15980170 L.Martínez, M.T.Sonoda, P.Webb, J.D.Baxter, M.S.Skaf, and I.Polikarpov (2005).
Molecular dynamics simulations reveal multiple pathways of ligand dissociation from thyroid hormone receptors.
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14990788 D.Bishop-Bailey, D.T.Walsh, and T.D.Warner (2004).
Expression and activation of the farnesoid X receptor in the vasculature.
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15246430 G.Benoit, M.Malewicz, and T.Perlmann (2004).
Digging deep into the pockets of orphan nuclear receptors: insights from structural studies.
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15330745 T.Claudel, E.Sturm, F.Kuipers, and B.Staels (2004).
The farnesoid X receptor: a novel drug target?
  Expert Opin Investig Drugs, 13, 1135-1148.  
12912852 A.F.Hofmann (2003).
Inappropriate ileal conservation of bile acids in cholestatic liver disease: homeostasis gone awry.
  Gut, 52, 1239-1241.  
12941427 C.P.Austin (2003).
The completed human genome: implications for chemical biology.
  Curr Opin Chem Biol, 7, 511-515.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.