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- PDB-5vo4: Crystal Structure Of The Androgen Receptor Ligand Binding Domain ... -

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Basic information

Entry
Database: PDB / ID: 5vo4
TitleCrystal Structure Of The Androgen Receptor Ligand Binding Domain In Complex With 5-(2-fluoro-4-hydroxyphenyl)-1-methyl-1H-pyrrole-2-carbonitrile
ComponentsAndrogen receptor
KeywordsHORMONE RECEPTOR / receptor / small molecule inhibitor
Function / homology
Function and homology information


POU domain binding / positive regulation of integrin biosynthetic process / cellular response to testosterone stimulus / androgen binding / androgen receptor signaling pathway / membraneless organelle assembly / RNA polymerase II general transcription initiation factor binding / cellular response to steroid hormone stimulus / nuclear steroid receptor activity / RUNX2 regulates osteoblast differentiation ...POU domain binding / positive regulation of integrin biosynthetic process / cellular response to testosterone stimulus / androgen binding / androgen receptor signaling pathway / membraneless organelle assembly / RNA polymerase II general transcription initiation factor binding / cellular response to steroid hormone stimulus / nuclear steroid receptor activity / RUNX2 regulates osteoblast differentiation / positive regulation of transcription by RNA polymerase III / cellular response to estrogen stimulus / estrogen response element binding / RNA polymerase II core promoter sequence-specific DNA binding / regulation of protein localization to plasma membrane / estrogen receptor signaling pathway / intracellular receptor signaling pathway / steroid binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / negative regulation of extrinsic apoptotic signaling pathway / RNA polymerase II transcription regulatory region sequence-specific DNA binding / SUMOylation of intracellular receptors / positive regulation of cell differentiation / male gonad development / molecular condensate scaffold activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Nuclear Receptor transcription pathway / positive regulation of miRNA transcription / beta-catenin binding / nuclear receptor activity / transcription coactivator binding / cell-cell signaling / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / molecular adaptor activity / RNA polymerase II-specific DNA-binding transcription factor binding / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear speck / transcription cis-regulatory region binding / Ub-specific processing proteases / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / negative regulation of cell population proliferation / signaling receptor binding / positive regulation of gene expression / chromatin binding / positive regulation of cell population proliferation / positive regulation of DNA-templated transcription / chromatin / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / DNA-templated transcription / nucleoplasm / zinc ion binding / nucleus / plasma membrane / cytosol / cytoplasm
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-9FG / Androgen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.35 Å
AuthorsParris, K. / Unwalla, R.
CitationJournal: J. Med. Chem. / Year: 2017
Title: Structure-Based Approach To Identify 5-[4-Hydroxyphenyl]pyrrole-2-carbonitrile Derivatives as Potent and Tissue Selective Androgen Receptor Modulators.
Authors: Unwalla, R. / Mousseau, J.J. / Fadeyi, O.O. / Choi, C. / Parris, K. / Hu, B. / Kenney, T. / Chippari, S. / McNally, C. / Vishwanathan, K. / Kilbourne, E. / Thompson, C. / Nagpal, S. / ...Authors: Unwalla, R. / Mousseau, J.J. / Fadeyi, O.O. / Choi, C. / Parris, K. / Hu, B. / Kenney, T. / Chippari, S. / McNally, C. / Vishwanathan, K. / Kilbourne, E. / Thompson, C. / Nagpal, S. / Wrobel, J. / Yudt, M. / Morris, C.A. / Powell, D. / Gilbert, A.M. / Chekler, E.L.P.
History
DepositionMay 2, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 14, 2018Provider: repository / Type: Initial release
Revision 1.1Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Androgen receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,3902
Polymers29,1741
Non-polymers2161
Water1,56787
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)55.123, 66.136, 70.183
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: 29174.199 Da / Num. of mol.: 1 / Fragment: UNP residues 671-920
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4
Production host: Escherichia coli-Pichia pastoris shuttle vector pPpARG4 (others)
References: UniProt: P10275
#2: Chemical ChemComp-9FG / 5-(2-fluoro-4-hydroxyphenyl)-1-methyl-1H-pyrrole-2-carbonitrile


Mass: 216.211 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H9FN2O
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 87 / 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: 2.24 Å3/Da / Density % sol: 45.12 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop / Details: 30% PEG400, HEPES pH 7, 200mM Ca Cl

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.54 Å
DetectorType: RIGAKU SATURN 92 / Detector: CCD / Date: Oct 10, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.35→36.26 Å / Num. obs: 11169 / % possible obs: 99.5 % / Redundancy: 3.7 % / Rsym value: 0.115 / Net I/σ(I): 25

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Processing

Software
NameVersionClassification
REFMAC5.5.0072refinement
DENZOdata reduction
DENZOdata scaling
PHASERphasing
RefinementResolution: 2.35→36.26 Å / Cor.coef. Fo:Fc: 0.927 / Cor.coef. Fo:Fc free: 0.885 / SU B: 9.303 / SU ML: 0.221 / Cross valid method: THROUGHOUT / ESU R: 0.542 / ESU R Free: 0.302 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2823 530 4.8 %RANDOM
Rwork0.22598 ---
obs0.22862 10587 99.45 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso mean: 29.717 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2--0.01 Å20 Å2
3----0.07 Å2
Refinement stepCycle: 1 / Resolution: 2.35→36.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1984 0 16 87 2087
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0222087
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9711.9572828
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5545250
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.71923.78995
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.88815365
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.3741511
X-RAY DIFFRACTIONr_chiral_restr0.0690.2308
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211578
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4421.51250
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.84422028
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.0823837
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8554.5800
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.349→2.41 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.334 35 -
Rwork0.252 735 -
obs--94.83 %

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