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Yorodumi- PDB-2yhd: Human androgen receptor in complex with AF2 small molecule inhibitor -
+Open data
-Basic information
Entry | Database: PDB / ID: 2yhd | ||||||
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Title | Human androgen receptor in complex with AF2 small molecule inhibitor | ||||||
Components | ANDROGEN RECEPTOR | ||||||
Keywords | TRANSCRIPTION / ACTIVATION FUNCTION 2 SITE (AF2) / SMALL MOLECULE INHIBITOR | ||||||
Function / homology | Function and homology information male somatic sex determination / : / lateral sprouting involved in mammary gland duct morphogenesis / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / intracellular receptor signaling pathway / tertiary branching involved in mammary gland duct morphogenesis ...male somatic sex determination / : / lateral sprouting involved in mammary gland duct morphogenesis / POU domain binding / negative regulation of integrin biosynthetic process / regulation of developmental growth / male genitalia morphogenesis / positive regulation of integrin biosynthetic process / intracellular receptor signaling pathway / tertiary branching involved in mammary gland duct morphogenesis / animal organ formation / 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 / membraneless organelle assembly / prostate gland epithelium morphogenesis / cellular response to testosterone stimulus / RNA polymerase II general transcription initiation factor binding / positive regulation of insulin-like growth factor receptor signaling pathway / positive regulation of intracellular estrogen receptor signaling pathway / positive regulation of transcription by RNA polymerase III / cellular response to steroid hormone stimulus / morphogenesis of an epithelial fold / seminiferous tubule development / androgen receptor signaling pathway / RUNX2 regulates osteoblast differentiation / single fertilization / mammary gland alveolus development / regulation of protein localization to plasma membrane / cellular response to estrogen stimulus / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / positive regulation of phosphorylation / estrogen receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / insulin-like growth factor receptor signaling pathway / epithelial cell proliferation / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of cell differentiation / G protein-coupled receptor activity / SUMOylation of intracellular receptors / molecular condensate scaffold activity / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / multicellular organism growth / transcription coactivator binding / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / beta-catenin binding / nuclear receptor activity / male gonad development / negative regulation of epithelial cell proliferation / MAPK cascade / cell-cell signaling / positive regulation of NF-kappaB transcription factor activity / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / spermatogenesis / RNA polymerase II-specific DNA-binding transcription factor binding / in utero embryonic development / transcription by RNA polymerase II / positive regulation of MAPK cascade / molecular adaptor activity / transcription cis-regulatory region binding / DNA-binding transcription factor activity, RNA polymerase II-specific / Ub-specific processing proteases / nuclear speck / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of cell population proliferation / signaling receptor binding / chromatin binding / positive regulation of cell population proliferation / positive regulation of gene expression / chromatin / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | AxerioCilies, P. / Lack, N.A. / ShashiNayana, M.R. / Chan, K.H. / Yeung, A. / LeBlanc, E. / Guns, E. / Rennie, P. / Cherkasov, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2011 Title: Inhibitors of Androgen Receptor Activation Function-2 (Af2) Site Identified Through Virtual Screening. Authors: Axerio-Cilies, P. / Lack, N.A. / Nayana, M.R. / Chan, K.H. / Yeung, A. / Leblanc, E. / Guns, E.S. / Rennie, P.S. / Cherkasov, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2yhd.cif.gz | 65.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2yhd.ent.gz | 47.5 KB | Display | PDB format |
PDBx/mmJSON format | 2yhd.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2yhd_validation.pdf.gz | 935.2 KB | Display | wwPDB validaton report |
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Full document | 2yhd_full_validation.pdf.gz | 940.3 KB | Display | |
Data in XML | 2yhd_validation.xml.gz | 12.4 KB | Display | |
Data in CIF | 2yhd_validation.cif.gz | 15.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/2yhd ftp://data.pdbj.org/pub/pdb/validation_reports/yh/2yhd | HTTPS FTP |
-Related structure data
Related structure data | 2am9S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 29046.074 Da / Num. of mol.: 1 / Fragment: LIGAND BINDING DOMAIN, RESIDUES 671-919 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P10275 |
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#2: Chemical | ChemComp-SO4 / |
#3: Chemical | ChemComp-TES / |
#4: Chemical | ChemComp-AV6 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 47.4 % / Description: NONE |
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Crystal grow | pH: 7.5 Details: 0.35 M NA2HPO4/K2HPO4, 0.1 M (NH4)2HPO4, 7.0% PEG 400, 50 MM TRIS-HCL, PH 7.5. |
-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD |
Radiation | Monochromator: ASYMMETRIC CUT SINGLE CRYSTAL SI(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→49.5 Å / Num. obs: 14010 / % possible obs: 98.8 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.2→2.26 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.5 / % possible all: 90.5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2AM9 Resolution: 2.2→49.47 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.915 / SU B: 6.45 / SU ML: 0.163 / Cross valid method: THROUGHOUT / ESU R: 0.283 / ESU R Free: 0.224 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.076 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→49.47 Å
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