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- PDB-3v49: Structure of ar lbd with activator peptide and sarm inhibitor 1 -

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Basic information

Entry
Database: PDB / ID: 3v49
TitleStructure of ar lbd with activator peptide and sarm inhibitor 1
Components
  • Androgen receptor
  • Androgen receptor, activator peptide
KeywordsTRANSCRIPTION / DIARYLHYDANTOIN / SYNTHESIS / SARM / ANTIANDROGEN / LIGAND BINDING DOMAIN / testosterone / Dihydrotestosterone / SARM (Selective Androgen Receptor Modulator)
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
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 ...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-PK0 / Androgen receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.7 Å
AuthorsNique, F. / Hebbe, S. / Peixoto, C. / Annoot, D. / Lefrancois, J.-M. / Duval, E. / Michoux, L. / Triballeau, N. / Lemoullec, J.-M. / Mollat, P. ...Nique, F. / Hebbe, S. / Peixoto, C. / Annoot, D. / Lefrancois, J.-M. / Duval, E. / Michoux, L. / Triballeau, N. / Lemoullec, J.-M. / Mollat, P. / Thauvin, M. / Prange, T. / Minet, D. / Clement-Lacroix, P. / Robin-Jagerschmidt, C. / Fleury, D. / Guedin, D. / Deprez, P.
CitationJournal: J.Med.Chem. / Year: 2012
Title: Discovery of diarylhydantoins as new selective androgen receptor modulators.
Authors: Nique, F. / Hebbe, S. / Peixoto, C. / Annoot, D. / Lefrancois, J.-M. / Duval, E. / Michoux, L. / Triballeau, N. / Lemoullec, J.M. / Mollat, P. / Thauvin, M. / Prange, T. / Minet, D. / ...Authors: Nique, F. / Hebbe, S. / Peixoto, C. / Annoot, D. / Lefrancois, J.-M. / Duval, E. / Michoux, L. / Triballeau, N. / Lemoullec, J.M. / Mollat, P. / Thauvin, M. / Prange, T. / Minet, D. / Clement-Lacroix, P. / Robin-Jagerschmidt, C. / Fleury, D. / Guedin, D. / Deprez, P.
History
DepositionDec 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 19, 2012Group: Database references
Revision 1.2Oct 8, 2014Group: Structure summary
Revision 1.3Aug 31, 2016Group: Other
Revision 1.4Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.5Sep 13, 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_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

Downloads & links

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Assembly

Deposited unit
A: Androgen receptor
B: Androgen receptor, activator peptide
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,7494
Polymers32,2642
Non-polymers4852
Water4,288238
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1280 Å2
ΔGint-22 kcal/mol
Surface area12090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.629, 67.331, 69.809
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: 30996.188 Da / Num. of mol.: 1 / Fragment: unp residues 654-919
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: AR, DHTR, NR3C4 / Production host: Escherichia coli (E. coli) / References: UniProt: P10275
#2: Protein/peptide Androgen receptor, activator peptide / Dihydrotestosterone receptor / Nuclear receptor subfamily 3 group C member 4


Mass: 1267.413 Da / Num. of mol.: 1 / Fragment: unp residues 21-31 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: P10275
#3: Chemical ChemComp-PK0 / 4-[(4R)-4-(4-hydroxyphenyl)-3,4-dimethyl-2,5-dioxoimidazolidin-1-yl]-2-(trifluoromethyl)benzonitrile


Mass: 389.328 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C19H14F3N3O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 238 / 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: 2

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Sample preparation

CrystalDensity Matthews: 1.84 Å3/Da / Density % sol: 38.18 %
Crystal growTemperature: 291 K / pH: 7.5
Details: Hanging drop set up as a 50:50 mixture of 1 microL protein+1 microL reservoir with: A) protein solution = 80 microL hAR LBD (3.5 mg/ml) + 1.5 microL activator undecapeptide (GAFQNLFQSVR)+1 ...Details: Hanging drop set up as a 50:50 mixture of 1 microL protein+1 microL reservoir with: A) protein solution = 80 microL hAR LBD (3.5 mg/ml) + 1.5 microL activator undecapeptide (GAFQNLFQSVR)+1 microL LiSO4 (0.2 M) in HEPES buffer 0.1 M + 0.5 mg inhibitor 1 (PK0) B) Reservoir = 1 ml HEPES buffer 0.1 M + PEG 4000 12-20 %, pH 7.5, VAPOR DIFFUSION, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength
SYNCHROTRONESRF BM30A10.934
2
Detector
TypeIDDetectorDate
ADSC QUANTUM 315r1CCDDec 12, 2007
2Jan 10, 2008
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SI(111)SINGLE WAVELENGTHMx-ray1
2SINGLE WAVELENGTHx-ray1
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.7→34.9 Å / Num. obs: 28211 / % possible obs: 98.3 % / Observed criterion σ(I): 4 / Redundancy: 4.5 % / Rmerge(I) obs: 0.043 / Net I/σ(I): 29.6
Reflection shellResolution: 1.7→1.8 Å / Redundancy: 4 % / Rmerge(I) obs: 0.185 / Mean I/σ(I) obs: 6.5 / % possible all: 97.6

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
SHELXmodel building
SHELXL-97refinement
MOSFLMdata reduction
SCALAdata scaling
SHELXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 2AMA

2ama


Resolution: 1.7→34 Å / Num. parameters: 9595 / Num. restraintsaints: 8954 / Cross valid method: THROUGHOUT / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflection
all0.193 28377 -
obs0.185 -97.9 %
Refine analyzeNum. disordered residues: 7 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2362
Refinement stepCycle: LAST / Resolution: 1.7→34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 33 238 2355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.011
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.025
X-RAY DIFFRACTIONs_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.046
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.023
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.071
X-RAY DIFFRACTIONs_approx_iso_adps0

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