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- PDB-4ny9: Crystal Structure Of the Human PXR-LBD In Complex With N-{(2R)-1-... -

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Basic information

Entry
Database: PDB / ID: 4ny9
TitleCrystal Structure Of the Human PXR-LBD In Complex With N-{(2R)-1-[(4S)-4-(4-chlorophenyl)-4-hydroxy-3,3-dimethylpiperidin-1-yl]-3-methyl-1-oxobutan-2-yl}-3-hydroxy-3-methylbutanamide
ComponentsNuclear receptor subfamily 1 group I member 2
KeywordsTRANSCRIPTION/TRANSCRIPTION inhibitor / pregnane X receptor / PXR / ligand binding domain / steroid receptor coactivator-1 / CCR1 / Chemokine Receptor-1 / NR / nuclear receptor / AF / activation function / MDR1 / multi-drug resistance gene-1 / TRANSCRIPTION-TRANSCRIPTION inhibitor complex
Function / homology
Function and homology information


intermediate filament cytoskeleton / xenobiotic transport / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity ...intermediate filament cytoskeleton / xenobiotic transport / steroid metabolic process / xenobiotic catabolic process / xenobiotic metabolic process / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / cell differentiation / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / regulation of DNA-templated transcription / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
: / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / Nuclear hormone receptors DNA-binding domain profile. / c4 zinc finger in nuclear hormone receptors / Nuclear hormone receptor, ligand-binding domain ...: / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Zinc finger, C4 type (two domains) / 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-2Q4 / Nuclear receptor subfamily 1 group I member 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsKhan, J.A. / Camac, D.M.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Discovery of the CCR1 antagonist, BMS-817399, for the treatment of rheumatoid arthritis.
Authors: Santella, J.B. / Gardner, D.S. / Duncia, J.V. / Wu, H. / Dhar, M. / Cavallaro, C. / Tebben, A.J. / Carter, P.H. / Barrish, J.C. / Yarde, M. / Briceno, S.W. / Cvijic, M.E. / Grafstrom, R.R. / ...Authors: Santella, J.B. / Gardner, D.S. / Duncia, J.V. / Wu, H. / Dhar, M. / Cavallaro, C. / Tebben, A.J. / Carter, P.H. / Barrish, J.C. / Yarde, M. / Briceno, S.W. / Cvijic, M.E. / Grafstrom, R.R. / Liu, R. / Patel, S.R. / Watson, A.J. / Yang, G. / Rose, A.V. / Vickery, R.D. / Caceres-Cortes, J. / Caporuscio, C. / Camac, D.M. / Khan, J.A. / An, Y. / Foster, W.R. / Davies, P. / Hynes, J.
History
DepositionDec 10, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 27, 2014Provider: repository / Type: Initial release
Revision 1.1Dec 10, 2014Group: Database references
Revision 1.2Nov 22, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor subfamily 1 group I member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,9793
Polymers33,4481
Non-polymers5312
Water27015
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Nuclear receptor subfamily 1 group I member 2
hetero molecules

A: Nuclear receptor subfamily 1 group I member 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)67,9586
Polymers66,8962
Non-polymers1,0624
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_555-y,-x,-z+1/21
Buried area1810 Å2
ΔGint-8 kcal/mol
Surface area26290 Å2
MethodPISA
Unit cell
Length a, b, c (Å)91.760, 91.760, 85.651
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein Nuclear receptor subfamily 1 group I member 2 / Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and ...Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and xenobiotic receptor / SXR


Mass: 33447.750 Da / Num. of mol.: 1 / Fragment: unp residues 142-431
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR / Plasmid: pCO7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: O75469
#2: Chemical ChemComp-2Q4 / N-{(2R)-1-[(4S)-4-(4-chlorophenyl)-4-hydroxy-3,3-dimethylpiperidin-1-yl]-3-methyl-1-oxobutan-2-yl}-3-hydroxy-3-methylbutanamide


Mass: 438.988 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H35ClN2O4
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 15 / 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: 2.69 Å3/Da / Density % sol: 58.6 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 7.8
Details: 0.1M imidazole, 8-10%(V/V)isopropanol. Apo crystal was soaked with 5 mM compound and Crystals harvested next day using 32% ethylene glycol as cryoprotectant, pH 7.8, VAPOR DIFFUSION, HANGING ...Details: 0.1M imidazole, 8-10%(V/V)isopropanol. Apo crystal was soaked with 5 mM compound and Crystals harvested next day using 32% ethylene glycol as cryoprotectant, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 / Wavelength: 1 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Mar 21, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
111
211
ReflectionResolution: 2.8→50 Å / Num. obs: 9474 / % possible obs: 99.8 % / Observed criterion σ(I): 0 / Redundancy: 6.6 % / Rmerge(I) obs: 0.115 / Net I/σ(I): 17

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Processing

Software
NameVersionClassificationNB
BUSTER-TNTREFMAC 5.2.0019refinement
PDB_EXTRACT3.11data extraction
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→45.88 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.894 / Occupancy max: 1 / Occupancy min: 1 / SU B: 15.481 / SU ML: 0.322 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.811 / ESU R Free: 0.418 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2982 450 4.8 %RANDOM
Rwork0.2283 ---
obs0.2316 9443 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 96.15 Å2 / Biso mean: 60.0612 Å2 / Biso min: 36.81 Å2
Baniso -1Baniso -2Baniso -3
1-0.01 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.02 Å2
Refinement stepCycle: LAST / Resolution: 2.8→45.88 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2127 0 36 15 2178
LS refinement shellResolution: 2.801→2.874 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.319 42 -
Rwork0.259 640 -
all-682 -
obs--99.13 %

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