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- PDB-2ihq: Crystal Structure of the Rat Androgen Receptor Ligand Binding Dom... -

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Basic information

Entry
Database: PDB / ID: 2ihq
TitleCrystal Structure of the Rat Androgen Receptor Ligand Binding Domian Complex with an N-Aryl-Hydroxybicyclohydantoin
ComponentsAndrogen receptor
KeywordsHORMONE/GROWTH FACTOR / ANDROGEN RECEPTOR / STEROID RECEPTOR / NUCLEAR RECEPTOR / TRANSCRIPTION REGULATION / LIGAND-BINDING DOMAIN / HORMONE-GROWTH FACTOR COMPLEX
Function / homology
Function and homology information


reproductive behavior / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / copulation / male sex differentiation / skeletal muscle hypertrophy / regulation of prostatic bud formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of penile erection / ribonucleotide binding / reproductive system development ...reproductive behavior / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / copulation / male sex differentiation / skeletal muscle hypertrophy / regulation of prostatic bud formation / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / positive regulation of penile erection / ribonucleotide binding / reproductive system development / male courtship behavior / Ub-specific processing proteases / male somatic sex determination / activation of prostate induction by androgen receptor signaling pathway / lateral sprouting involved in mammary gland duct morphogenesis / SUMOylation of intracellular receptors / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / reproductive structure development / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / Nuclear Receptor transcription pathway / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / cellular response to follicle-stimulating hormone stimulus / androgen binding / 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 / intracellular receptor signaling pathway / cellular response to testosterone stimulus / fertilization / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of transcription by RNA polymerase III / positive regulation of intracellular estrogen receptor signaling pathway / nuclear androgen receptor binding / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / response to testosterone / seminiferous tubule development / androgen receptor signaling pathway / single fertilization / mammary gland alveolus development / regulation of protein localization to plasma membrane / estrogen receptor signaling pathway / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of phosphorylation / steroid binding / insulin-like growth factor receptor signaling pathway / epithelial cell proliferation / positive regulation of cell differentiation / negative regulation of extrinsic apoptotic signaling pathway / response to insulin / multicellular organism growth / beta-catenin binding / transcription coactivator binding / positive regulation of miRNA transcription / nuclear receptor activity / negative regulation of epithelial cell proliferation / male gonad development / MAPK cascade / response to estradiol / positive regulation of NF-kappaB transcription factor activity / ATPase binding / spermatogenesis / regulation of gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / in utero embryonic development / RNA polymerase II-specific DNA-binding transcription factor binding / sequence-specific DNA binding / transcription by RNA polymerase II / positive regulation of MAPK cascade / molecular adaptor activity / transcription cis-regulatory region binding / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / protein domain specific binding / negative regulation of cell population proliferation / axon / signaling receptor binding / negative regulation of DNA-templated transcription / chromatin binding / dendrite / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / enzyme binding / negative regulation of transcription by RNA polymerase II
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 / 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 ...Androgen receptor / Androgen receptor / Retinoid X Receptor / Retinoid X 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-LG7 / Androgen receptor
Similarity search - Component
Biological speciesRattus norvegicus (Norway rat)
MethodX-RAY DIFFRACTION / molecular replacement / Resolution: 2 Å
AuthorsSack, J.S.
CitationJournal: J.Med.Chem. / Year: 2006
Title: Discovery of potent, orally-active, and muscle-selective androgen receptor modulators based on an N-aryl-hydroxybicyclohydantoin scaffold.
Authors: Sun, C. / Robl, J.A. / Wang, T.C. / Huang, Y. / Kuhns, J.E. / Lupisella, J.A. / Beehler, B.C. / Golla, R. / Sleph, P.G. / Seethala, R. / Fura, A. / Krystek, S.R. / An, Y. / Malley, M.F. / ...Authors: Sun, C. / Robl, J.A. / Wang, T.C. / Huang, Y. / Kuhns, J.E. / Lupisella, J.A. / Beehler, B.C. / Golla, R. / Sleph, P.G. / Seethala, R. / Fura, A. / Krystek, S.R. / An, Y. / Malley, M.F. / Sack, J.S. / Salvati, M.E. / Grover, G.J. / Ostrowski, J. / Hamann, L.G.
History
DepositionSep 27, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 30, 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 / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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)30,5902
Polymers30,2821
Non-polymers3071
Water1,36976
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.546, 65.522, 70.013
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


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 / Plasmid: PET28B / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: P15207
#2: Chemical ChemComp-LG7 / 4-[(7R,7AS)-7-HYDROXY-1,3-DIOXOTETRAHYDRO-1H-PYRROLO[1,2-C]IMIDAZOL-2(3H)-YL]-1-NAPHTHONITRILE


Mass: 307.303 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H13N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 76 / 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: 2.06 Å3/Da / Density % sol: 40.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 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: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.54 / Wavelength: 1.54 Å
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jan 25, 2001 / Details: "BLUE" CONFOCAL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2→25 Å / Num. obs: 15426 / % possible obs: 87.5 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Biso Wilson estimate: 32.831 Å2 / Rmerge(I) obs: 0.077 / Net I/σ(I): 13.2
Reflection shellResolution: 2→2.07 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 1.7 / % possible all: 49

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
BUSTER-TNT1.9.3refinement
RefinementMethod to determine structure: molecular replacement
Starting model: 1I37

1i37


Resolution: 2→25 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.2685 769 4.99 %RANDOM
Rwork0.2058 ---
obs0.2089 15399 --
Displacement parametersBiso mean: 43.6 Å2
Baniso -1Baniso -2Baniso -3
1--20.09285176 Å20 Å20 Å2
2--6.84117303 Å20 Å2
3---13.25167873 Å2
Refine analyzeLuzzati coordinate error obs: 0.2854 Å
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2007 0 23 76 2106
Refine LS restraints
Refine-IDTypeDev idealNumberWeight
X-RAY DIFFRACTIONt_bond_d0.00520842
X-RAY DIFFRACTIONt_angle_deg0.7928102
X-RAY DIFFRACTIONt_dihedral_angle_d23.9274300
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes0.005552
X-RAY DIFFRACTIONt_gen_planes0.0093105
X-RAY DIFFRACTIONt_it1.856208520
X-RAY DIFFRACTIONt_nbd0.036295
LS refinement shellResolution: 2→2.12 Å / Total num. of bins used: 9
RfactorNum. reflection% reflection
Rfree0.2951 73 4.7 %
Rwork0.2535 1481 -
obs--87.73 %

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