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- PDB-3g0w: Crystal structure of the rat androgen receptor ligand binding dom... -

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Basic information

Entry
Database: PDB / ID: 3g0w
TitleCrystal structure of the rat androgen receptor ligand binding domain complex with an n-aryl-oxazolidin 2-imine inhibitor
ComponentsAndrogen receptor
KeywordsHORMONE / ANDROGEN RECEPTOR / STEROID RECEPTOR / NUCLEAR RECEPTOR / TRANSCRIPTION REGULATION / LIGAND-BINDING DOMAIN / Disease mutation / DNA-binding / Lipid-binding / Metal-binding / Nucleus / Phosphoprotein / Receptor / Steroid-binding / Transcription / Ubl conjugation / Zinc / Zinc-finger / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


reproductive behavior / positive regulation of hippocampal neuron apoptotic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / copulation / positive regulation of locomotion / male sex differentiation / skeletal muscle hypertrophy / positive regulation of penile erection / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / regulation of prostatic bud formation ...reproductive behavior / positive regulation of hippocampal neuron apoptotic process / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / copulation / positive regulation of locomotion / male sex differentiation / skeletal muscle hypertrophy / positive regulation of penile erection / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / regulation of prostatic bud formation / ribonucleotide binding / male courtship behavior / male somatic sex determination / prostate induction / lateral sprouting involved in mammary gland duct morphogenesis / Ub-specific processing proteases / male genitalia morphogenesis / reproductive system development / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / positive regulation of integrin biosynthetic process / reproductive structure development / SUMOylation of intracellular receptors / tertiary branching involved in mammary gland duct morphogenesis / Nuclear Receptor transcription pathway / animal organ formation / drinking behavior / androgen binding / cellular response to follicle-stimulating hormone stimulus / response to environmental enrichment / Leydig cell differentiation / regulation of systemic arterial blood pressure / epithelial cell morphogenesis / prostate gland growth / epithelial cell differentiation involved in prostate gland development / positive regulation of epithelial cell proliferation involved in prostate gland development / prostate gland epithelium morphogenesis / cellular response to testosterone stimulus / locomotion / membraneless organelle assembly / fertilization / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / response to steroid hormone / positive regulation of transcription by RNA polymerase III / nuclear androgen receptor binding / morphogenesis of an epithelial fold / cellular response to steroid hormone stimulus / positive regulation of intracellular estrogen receptor signaling pathway / response to muscle activity / seminiferous tubule development / response to testosterone / androgen receptor signaling pathway / cellular response to estrogen stimulus / mammary gland alveolus development / single fertilization / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of phosphorylation / regulation of protein localization to plasma membrane / RNA polymerase II core promoter sequence-specific DNA binding / intracellular receptor signaling pathway / estrogen receptor signaling pathway / steroid binding / insulin-like growth factor receptor signaling pathway / liver regeneration / epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / response to insulin / response to nicotine / molecular condensate scaffold activity / transcription coactivator binding / beta-catenin binding / multicellular organism growth / positive regulation of miRNA transcription / nuclear matrix / nuclear receptor activity / male gonad development / negative regulation of epithelial cell proliferation / positive regulation of NF-kappaB transcription factor activity / MAPK cascade / response to estradiol / ATPase binding / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / gene expression / spermatogenesis / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / in utero embryonic development / response to ethanol / transcription by RNA polymerase II / transcription cis-regulatory region binding / positive regulation of MAPK cascade / nuclear speck / protein domain specific binding / RNA polymerase II cis-regulatory region sequence-specific DNA binding
Similarity search - Function
Androgen receptor / Androgen receptor / : / Retinoid X Receptor / Retinoid X 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 ...Androgen receptor / Androgen receptor / : / Retinoid X Receptor / Retinoid X 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-LGB / Androgen receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / SYNCHROTRON / molecular replacement / Resolution: 1.95 Å
AuthorsSack, J.S.
CitationJournal: J.Med.Chem. / Year: 2009
Title: N-aryl-oxazolidin-2-imine muscle selective androgen receptor modulators enhance potency through pharmacophore reorientation.
Authors: Nirschl, A.A. / Zou, Y. / Krystek, S.R. / Sutton, J.C. / Simpkins, L.M. / Lupisella, J.A. / Kuhns, J.E. / Seethala, R. / Golla, R. / Sleph, P.G. / Beehler, B.C. / Grover, G.J. / Egan, D. / ...Authors: Nirschl, A.A. / Zou, Y. / Krystek, S.R. / Sutton, J.C. / Simpkins, L.M. / Lupisella, J.A. / Kuhns, J.E. / Seethala, R. / Golla, R. / Sleph, P.G. / Beehler, B.C. / Grover, G.J. / Egan, D. / Fura, A. / Vyas, V.P. / Li, Y.X. / Sack, J.S. / Kish, K.F. / An, Y. / Bryson, J.A. / Gougoutas, J.Z. / DiMarco, J. / Zahler, R. / Ostrowski, J. / Hamann, L.G.
History
DepositionJan 29, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 28, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _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: Androgen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,6422
Polymers30,2821
Non-polymers3601
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)54.862, 65.739, 69.750
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Androgen receptor / Dihydrotestosterone receptor / Nuclear receptor subfamily 3 group C member 4


Mass: 30282.414 Da / Num. of mol.: 1 / Fragment: Ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Rattus norvegicus (Norway rat) / Gene: Ar, Nr3c4 / Plasmid: pET28b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-DE3 / References: UniProt: P15207
#2: Chemical ChemComp-LGB / 2-chloro-4-{[(1R,3Z,7S,7aS)-7-hydroxy-1-(trifluoromethyl)tetrahydro-1H-pyrrolo[1,2-c][1,3]oxazol-3-ylidene]amino}-3-met hylbenzonitrile / 3,11-DIFLUORO-6,8,13-TRIMETHYL-8H-QUINO[4,3,2-KL]ACRIDIN-13-IUM


Mass: 359.731 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H13ClF3N3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.08 Å3/Da / Density % sol: 40.83 %
Crystal growDetails: 0.88M NA TARTRATE, 0.1M NA HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 32-ID / Wavelength: 1
DetectorType: MAR / Detector: CCD / Date: Dec 11, 2003 / Details: MICROMAX CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 18851 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 7.3 % / Biso Wilson estimate: 30.596 Å2 / Rmerge(I) obs: 0.085 / Net I/σ(I): 20.6
Reflection shellResolution: 1.95→2.02 Å / Redundancy: 7.6 % / Rmerge(I) obs: 0.452 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
AMoREphasing
BUSTER-TNT2.5.1refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: molecular replacement / Resolution: 1.95→47.84 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2382 669 3.58 %RANDOM
Rwork0.2 ---
obs0.2014 18689 98.34 %-
Displacement parametersBiso mean: 34.51 Å2
Baniso -1Baniso -2Baniso -3
1--7.63131135 Å20 Å20 Å2
2--8.55388617 Å20 Å2
3----0.92257482 Å2
Refinement stepCycle: LAST / Resolution: 1.95→47.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2034 0 24 171 2229
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00521112
X-RAY DIFFRACTIONt_angle_deg0.80628452
X-RAY DIFFRACTIONt_dihedral_angle_d20.9714230
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005482
X-RAY DIFFRACTIONt_gen_planes0.013005
X-RAY DIFFRACTIONt_it1.179211120
X-RAY DIFFRACTIONt_nbd0.032305
LS refinement shellResolution: 1.95→2.07 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.3411 109 3.77 %
Rwork0.2937 2779 -
all0.2953 2888 -
obs--98.34 %

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