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- PDB-6dxk: Glucocorticoid Receptor in complex with Compound 11 -

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Basic information

Entry
Database: PDB / ID: 6dxk
TitleGlucocorticoid Receptor in complex with Compound 11
ComponentsGlucocorticoid receptor
KeywordsTRANSCRIPTION / SIGNALING PROTEIN / NUCLEAR HORMONE RECEPTOR / LIGAND COMPLEX
Function / homology
Function and homology information


Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / glucocorticoid metabolic process / neuroinflammatory response / microglia differentiation / maternal behavior / mammary gland duct morphogenesis ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity / steroid hormone binding / PTK6 Expression / glucocorticoid metabolic process / neuroinflammatory response / microglia differentiation / maternal behavior / mammary gland duct morphogenesis / nucleus localization / astrocyte differentiation / cellular response to glucocorticoid stimulus / motor behavior / regulation of gluconeogenesis / adrenal gland development / cellular response to steroid hormone stimulus / estrogen response element binding / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / intracellular steroid hormone receptor signaling pathway / core promoter sequence-specific DNA binding / cellular response to transforming growth factor beta stimulus / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / TBP-class protein binding / steroid binding / cellular response to dexamethasone stimulus / synaptic transmission, glutamatergic / chromosome segregation / RNA polymerase II transcription regulatory region sequence-specific DNA binding / Hsp90 protein binding / SUMOylation of intracellular receptors / spindle / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Nuclear Receptor transcription pathway / Regulation of RUNX2 expression and activity / positive regulation of neuron apoptotic process / nuclear receptor activity / Circadian Clock / sequence-specific double-stranded DNA binding / gene expression / chromatin organization / DNA-binding transcription activator activity, RNA polymerase II-specific / Potential therapeutics for SARS / DNA-binding transcription factor activity, RNA polymerase II-specific / mitochondrial matrix / nuclear speck / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / cell division / centrosome / negative regulation of DNA-templated transcription / synapse / apoptotic process / chromatin / regulation of DNA-templated transcription / regulation of transcription by RNA polymerase II / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / RNA binding / zinc ion binding / nucleoplasm / membrane / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Glucocorticoid receptor / Glucocorticoid receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone 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 ...Glucocorticoid receptor / Glucocorticoid receptor / Retinoid X Receptor / Retinoid X Receptor / Nuclear hormone 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-HJ4 / Glucocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.05 Å
AuthorsRew, Y. / Du, X. / Eksterowicz, J. / Zhou, H. / Jahchan, N. / Zhu, L. / Yan, X. / Kawai, H. / McGee, L.R. / Medina, J.C. ...Rew, Y. / Du, X. / Eksterowicz, J. / Zhou, H. / Jahchan, N. / Zhu, L. / Yan, X. / Kawai, H. / McGee, L.R. / Medina, J.C. / Huang, T. / Chen, C. / Zavorotinskaya, T. / Sutimantanapi, D. / Waszczuk, J. / Jackson, E. / Huang, E. / Ye, Q. / Fantin, V.R. / Daqing, S.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Discovery of a Potent and Selective Steroidal Glucocorticoid Receptor Antagonist (ORIC-101).
Authors: Rew, Y. / Du, X. / Eksterowicz, J. / Zhou, H. / Jahchan, N. / Zhu, L. / Yan, X. / Kawai, H. / McGee, L.R. / Medina, J.C. / Huang, T. / Chen, C. / Zavorotinskaya, T. / Sutimantanapi, D. / ...Authors: Rew, Y. / Du, X. / Eksterowicz, J. / Zhou, H. / Jahchan, N. / Zhu, L. / Yan, X. / Kawai, H. / McGee, L.R. / Medina, J.C. / Huang, T. / Chen, C. / Zavorotinskaya, T. / Sutimantanapi, D. / Waszczuk, J. / Jackson, E. / Huang, E. / Ye, Q. / Fantin, V.R. / Sun, D.
History
DepositionJun 29, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 11, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Glucocorticoid receptor
B: Glucocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2784
Polymers59,3352
Non-polymers9432
Water543
1
A: Glucocorticoid receptor
hetero molecules

B: Glucocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,2784
Polymers59,3352
Non-polymers9432
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_455-x-1/2,-y,z+1/21
Buried area1960 Å2
ΔGint-14 kcal/mol
Surface area22870 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.193, 98.694, 100.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: HIS / End label comp-ID: HIS / Refine code: 0 / Auth seq-ID: 530 - 775 / Label seq-ID: 11 - 256

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Glucocorticoid receptor / / GR / Nuclear receptor subfamily 3 group C member 1


Mass: 29667.309 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C1, GRL / Production host: Escherichia coli (E. coli) / References: UniProt: P04150
#2: Chemical ChemComp-HJ4 / (8S,11R,13S,14S,17S)-11-[4-(dimethylamino)phenyl]-17-(3,3-dimethylbut-1-yn-1-yl)-17-hydroxy-13-methyl-1,2,6,7,8,11,12,13,14,15,16,17-dodecahydro-3H-cyclopenta[a]phenanthren-3-one (non-preferred name)


Mass: 471.673 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C32H41NO2 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 3 / 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: 3.53 Å3/Da / Density % sol: 65.18 %
Crystal growTemperature: 293 K / Method: vapor diffusion / Details: pH 6.75

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Apr 5, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 3.05→70.39 Å / Num. obs: 15142 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 17.7
Reflection shellResolution: 3.05→3.3 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.43 / Num. unique obs: 3103 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.8.0155refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1NHZ

1nhz


Resolution: 3.05→49.35 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.887 / SU B: 16.113 / SU ML: 0.294 / Cross valid method: THROUGHOUT / ESU R Free: 0.09 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25989 537 3.5 %RANDOM
Rwork0.21678 ---
obs0.21837 14605 97.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 60.618 Å2
Baniso -1Baniso -2Baniso -3
1--24.96 Å2-0 Å2-0 Å2
2--31.67 Å20 Å2
3----6.7 Å2
Refinement stepCycle: LAST / Resolution: 3.05→49.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4013 0 70 3 4086
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0194064
X-RAY DIFFRACTIONr_bond_other_d0.0020.023876
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.9865537
X-RAY DIFFRACTIONr_angle_other_deg1.17338862
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0355493
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.39224.251167
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.93115684
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1191517
X-RAY DIFFRACTIONr_chiral_restr0.0750.2633
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.024530
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02935
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_it8.1598.281978
X-RAY DIFFRACTIONr_mcbond_other8.1618.2781977
X-RAY DIFFRACTIONr_mcangle_it11.84514.0042469
X-RAY DIFFRACTIONr_mcangle_other11.84214.0072470
X-RAY DIFFRACTIONr_scbond_it8.3658.4472086
X-RAY DIFFRACTIONr_scbond_other8.3638.4462087
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other11.92614.0163069
X-RAY DIFFRACTIONr_long_range_B_refined14.38873.394403
X-RAY DIFFRACTIONr_long_range_B_other14.38673.3864404
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 15344 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.06 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 3.05→3.129 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.392 33 -
Rwork0.297 1042 -
obs--96.41 %

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