PDB-3e7c: Glucocorticoid Receptor LBD bound to GSK866

ID or keywords:

Entry

Database: PDB / ID: 3e7c

Title

Glucocorticoid Receptor LBD bound to GSK866

Components

Glucocorticoid receptor
Nuclear receptor coactivator 2

Keywords

TRANSCRIPTION / GR /

Glucocorticoid Receptor /

Nuclear Receptor / Alternative initiation / Chromatin regulator / Disease mutation / DNA-binding / Lipid-binding / Metal-binding /

Nucleus /

Phosphoprotein /

Pseudohermaphroditism / Receptor / Steroid-binding /

Transcription regulation /

Zinc-finger / Activator

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 / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis /

maternal behavior ...Regulation of NPAS4 gene transcription / regulation of glucocorticoid biosynthetic process / nuclear glucocorticoid receptor activity /

steroid hormone binding / PTK6 Expression / neuroinflammatory response / glucocorticoid metabolic process / microglia differentiation / mammary gland duct morphogenesis /

maternal behavior / astrocyte differentiation / cellular response to glucocorticoid stimulus /

motor behavior /

regulation of gluconeogenesis / adrenal gland development / RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding / cellular response to steroid hormone stimulus / locomotor rhythm /

aryl hydrocarbon receptor binding / regulation of lipid metabolic process / cellular response to Thyroglobulin triiodothyronine / regulation of glucose metabolic process / Synthesis of bile acids and bile salts / Endogenous sterols /

estrogen response element binding / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / FOXO-mediated transcription of oxidative stress, metabolic and neuronal genes / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / intracellular steroid hormone receptor signaling pathway / core promoter sequence-specific DNA binding / regulation of cellular response to insulin stimulus / Recycling of bile acids and salts / cellular response to hormone stimulus / cellular response to transforming growth factor beta stimulus / positive regulation of adipose tissue development / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / peroxisome proliferator activated receptor signaling pathway / RORA activates gene expression / TBP-class protein binding / Regulation of lipid metabolism by PPARalpha /

steroid binding / cellular response to dexamethasone stimulus / BMAL1:CLOCK,NPAS2 activates circadian gene expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / nuclear receptor coactivator activity /

synaptic transmission, glutamatergic / response to progesterone /

chromosome segregation /

nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding /

Hsp90 protein binding / circadian regulation of gene expression / Heme signaling / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3 / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / DNA-binding transcription repressor activity, RNA polymerase II-specific / positive regulation of miRNA transcription / Transcriptional regulation of white adipocyte differentiation / Nuclear Receptor transcription pathway / spindle / RNA polymerase II transcription regulator complex / Regulation of RUNX2 expression and activity /

nuclear receptor activity / positive regulation of neuron apoptotic process / sequence-specific double-stranded DNA binding /

Circadian Clock / chromatin organization / HATs acetylate histones /

gene expression / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression /

transcription regulator complex / Potential therapeutics for SARS /

transcription coactivator activity /

nuclear body /

protein dimerization activity / 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 / protein domain specific binding /

cell division / negative regulation of DNA-templated transcription /

centrosome / apoptotic process /

synapse /

chromatin binding /

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
Similarity search - Function

Glucocorticoid receptor /

Nuclear receptor coactivator 2 / Nuclear receptor coactivator 2/3, DUF4927 / Domain of unknown function (DUF4927) / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator ...
Similarity search - Domain/homology

Biological species

Homo sapiens (human)

Method

X-RAY DIFFRACTION /

SYNCHROTRON /

MOLECULAR REPLACEMENT /

molecular replacement / Resolution: 2.15 Å

Authors

Madauss, K.P. / Williams, S.P. / Mclay, I. / Stewart, E.L. / Bledsoe, R.K.

Citation

Journal: Bioorg.Med.Chem.Lett. / Year: 2008
Title: The first X-ray crystal structure of the glucocorticoid receptor bound to a non-steroidal agonist.
Authors: Madauss, K.P. / Bledsoe, R.K. / Mclay, I. / Stewart, E.L. / Uings, I.J. / Weingarten, G. / Williams, S.P.

History

Deposition	Aug 18, 2008	Deposition site: RCSB / Processing site: RCSB
Revision 1.0	Nov 25, 2008	Provider: repository / Type: Initial release
Revision 1.1	Jul 13, 2011	Group: Non-polymer description / Version format compliance
Revision 1.2	Apr 2, 2014	Group: Source and taxonomy
Revision 1.3	Oct 25, 2017	Group: Refinement description / Category: software
Revision 1.4	Oct 20, 2021	Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5	Feb 21, 2024	Group: Data collection / Category: chem_comp_atom / chem_comp_bond
Revision 1.6	Apr 3, 2024	Group: Refinement description / Category: pdbx_initial_refinement_model

Structure viewer	Molecule: MolmilJmol/JSmol

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Download

PDBx/mmCIF format	3e7c.cif.gz	224.5 KB	Display	PDBx/mmCIF format
PDB format	pdb3e7c.ent.gz	181.7 KB	Display	PDB format
PDBx/mmJSON format	3e7c.json.gz		Tree view	PDBx/mmJSON format
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Validation report

Arichive directory	https://data.pdbj.org/pub/pdb/validation_reports/e7/3e7c ftp://data.pdbj.org/pub/pdb/validation_reports/e7/3e7c	HTTPS FTP

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Related structure data

Related structure data	1m2z
Similar structure data	3k22-d 3riv-d 6bqt-4 6bd1-2 3p1q-1 5m37-d 6bcy-2 3cld-d 2h42-4 2odi-d Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Search similar-shape structures by Omokage search (details) Similarity search - Function & homologyF&H Search Similarity search - FunctionF&H Search Similarity search - HomologyF&H Search

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Links

PDB pages	PDBj / wwPDB / NCBI
Related items in Molecule of the Month	#258 - Jun 2021 Glucocorticoid Receptor and Dexamethasone similarity (34) #240 - Dec 2019 Hypoxia-Inducible Factors similarity (7) #122 - Feb 2010 Enhanceosome similarity (21) #207 - Mar 2017 Photoactive Yellow Protein similarity (2) #155 - Nov 2012 Vitamin D Receptor similarity (7) #194 - Feb 2016 Designer Insulins similarity (1) #92 - Aug 2007 Anabolic Steroids similarity (3) #112 - Apr 2009 Oct and Sox Transcription Factors similarity (4) #14 - Feb 2001 Insulin similarity (1) #37 - Jan 2003 Serum Albumin similarity (1) #183 - Mar 2015 Phototropin similarity (2) #190 - Oct 2015 Two-component Systems similarity (2) #149 - May 2012 Leptin similarity (1) #222 - Jun 2018 Proteins and Nanoparticles similarity (1) #57 - Sep 2004 Catalase similarity (1) #94 - Oct 2007 Superoxide Dismutase similarity (1) #202 - Oct 2016 Dipeptidyl Peptidase 4 similarity (1)

PDB pages

PDBj /

wwPDB /

NCBI

Related items in Molecule of the Month

#258 - Jun 2021
Glucocorticoid Receptor and Dexamethasone
similarity (34)
#240 - Dec 2019
Hypoxia-Inducible Factors
similarity (7)
#122 - Feb 2010
Enhanceosome
similarity (21)
#207 - Mar 2017
Photoactive Yellow Protein
similarity (2)
#155 - Nov 2012
Vitamin D Receptor
similarity (7)
#194 - Feb 2016
Designer Insulins
similarity (1)
#92 - Aug 2007
Anabolic Steroids
similarity (3)
#112 - Apr 2009
Oct and Sox Transcription Factors
similarity (4)
#14 - Feb 2001
Insulin
similarity (1)
#37 - Jan 2003
Serum Albumin
similarity (1)
#183 - Mar 2015
Phototropin
similarity (2)
#190 - Oct 2015
Two-component Systems
similarity (2)
#149 - May 2012
Leptin
similarity (1)
#222 - Jun 2018
Proteins and Nanoparticles
similarity (1)
#57 - Sep 2004
Catalase
similarity (1)
#94 - Oct 2007
Superoxide Dismutase
similarity (1)
#202 - Oct 2016
Dipeptidyl Peptidase 4
similarity (1)

Deposited unit

A: Glucocorticoid receptor

H: Nuclear receptor coactivator 2

B: Glucocorticoid receptor

D: Nuclear receptor coactivator 2

hetero molecules

63.8 kDa, 4 polymers
Search similar-shape structures of this assembly by Omokage search (details)

1

Idetical with deposited unit
defined by author&software

2

A: Glucocorticoid receptor

H: Nuclear receptor coactivator 2

hetero molecules

defined by software
31.8 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

3

B: Glucocorticoid receptor

D: Nuclear receptor coactivator 2

hetero molecules

defined by software
31.9 kDa, 2 polymers
Search similar-shape structures of this assembly by Omokage search (details)

Unit cell

Length a, b, c (Å)	126.654, 126.654, 78.991
Angle α, β, γ (deg.)	90.00, 90.00, 120.00
Int Tables number	169
Space group name H-M	P6₁

#1: Protein	Glucocorticoid receptor / / GR / Nuclear receptor subfamily 3 group C member 1 Mass: 29841.715 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 521-777 / Mutation: F602Y, C638G 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: Protein/peptide	Nuclear receptor coactivator 2 / / NCoA-2 / Transcriptional intermediary factor 2 Mass: 1349.576 Da / Num. of mol.: 2 / Fragment: UNP RESIDUES 741-751 / Source method: obtained synthetically / Source: (synth.) Homo sapiens (human) / References: UniProt: Q15596
#3: Chemical	ChemComp-866 / 5-amino-N-[(2S)-2-({[(2,6-dichlorophenyl)carbonyl](ethyl)amino}methyl)-3,3,3-trifluoro-2-hydroxypropyl]-1-(4-fluorophenyl)-1H-pyrazole-4-carboxamide Mass: 562.344 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C₂₃H₂₁Cl₂F₄N₅O₃
#4: Chemical	ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C₃H₈O₃
#5: Water	ChemComp-HOH / water / Water Mass: 18.015 Da / Num. of mol.: 93 / Source method: isolated from a natural source / Formula: H₂O

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Experiment

Experiment	Method: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

Crystal	Density Matthews: 2.93 Å³/Da / Density % sol: 58.05 %
Crystal grow	Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 0.1M MES pH 6.5, 1.6M MgSO4, 0.1% betahexaglucoside, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

Diffraction

Mean temperature: 100 K

Diffraction source

Source:

SYNCHROTRON / Site:

APS

/ Beamline: 17-ID / Wavelength: 0.97 Å

Detector

Type: ADSC QUANTUM 210 / Detector: CCD

Radiation

Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray

Radiation wavelength

Wavelength: 0.97 Å / Relative weight: 1

Reflection

Resolution: 2.15→50 Å / Num. obs: 37919 / % possible obs: 96.4 % / Redundancy: 8.2 % / R_merge(I) obs: 0.047 / Χ²: 0.91

Reflection shell

Resolution (Å)	Redundancy (%)	R_merge(I) obs	Num. unique all	Χ²	Diffraction-ID	% possible all
2.15-2.23	5.3	0.478	3585	0.741	1	91.7
2.23-2.32	6	0.43	3608	1.54	1	92.7
2.32-2.42	6.8	0.299	3581	0.73	1	91.7
2.42-2.55	7.7	0.228	3662	0.692	1	93.3
2.55-2.71	8.6	0.164	3757	0.812	1	95.4
2.71-2.92	9.2	0.113	3890	0.727	1	99.3
2.92-3.21	9.5	0.076	3908	0.775	1	100
3.21-3.68	9.5	0.044	3939	0.915	1	100
3.68-4.63	9.5	0.03	3953	1.027	1	100
4.63-50	9.2	0.029	4036	1.187	1	99.9

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Phasing

Phasing

Method:

molecular replacement

Phasing MR

Model details: Phaser MODE: MR_AUTO

	Highest resolution	Lowest resolution
Rotation	2.5 Å	19.91 Å
Translation	2.5 Å	19.91 Å

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Processing

Software

Name	Version	Classification
DENZO		data reduction
SCALEPACK		data scaling
PHASER		phasing
PHENIX		refinement
PDB_EXTRACT	3.006	data extraction
StructureStudio		data collection
HKL-2000		data reduction
HKL-2000		data scaling

Refinement

Method to determine structure:

MOLECULAR REPLACEMENT
Starting model: non public liganded GR LBD crystal structure at 2.2 A in P61 SG

Resolution: 2.15→19.909 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.712 / Stereochemistry target values: ml

	R_factor	Num. reflection	% reflection
R_free	0.266	2332	6.94 %
R_work	0.21	-	-
obs	-	33592	85.53 %

Solvent computation

B_sol: 73.129 Å² / k_sol: 0.312 e/Å³

Displacement parameters

B_iso max: 283.35 Å² / B_iso mean: 77.572 Å² / B_iso min: 27.19 Å²

	B_aniso -1	B_aniso -2	B_aniso -3
1-	-19.829 Å²	-0 Å²	0 Å²
2-	-	-19.829 Å²	0 Å²
3-	-	-	39.659 Å²

Refinement step

Cycle: LAST / Resolution: 2.15→19.909 Å

	Protein	Nucleic acid	Ligand	Solvent	Total
Num. atoms	4145	0	92	93	4330

Refine LS restraints

Refine-ID	Type	Dev ideal	Weight
X-RAY DIFFRACTION	f_angle_d	0.701	1
X-RAY DIFFRACTION	f_bond_d	0.005	1
X-RAY DIFFRACTION	f_chiral_restr	0.054	1
X-RAY DIFFRACTION	f_dihedral_angle_d	10.78	1
X-RAY DIFFRACTION	f_plane_restr	0.003	1
X-RAY DIFFRACTION	f_nbd_refined	4.059	1

LS refinement shell

Resolution (Å)	R_factor R_work	Num. reflection R_work	Refine-ID	Total num. of bins used	% reflection obs (%)
2.15-2.161	0.32	359	X-RAY DIFFRACTION	63	58
2.161-2.173	0.303	388	X-RAY DIFFRACTION	63	63
2.173-2.185	0.28	388	X-RAY DIFFRACTION	63	61
2.185-2.197	0.272	379	X-RAY DIFFRACTION	63	62
2.197-2.21	0.293	390	X-RAY DIFFRACTION	63	66
2.21-2.223	0.258	409	X-RAY DIFFRACTION	63	64
2.223-2.236	0.298	370	X-RAY DIFFRACTION	63	61
2.236-2.249	0.312	393	X-RAY DIFFRACTION	63	62
2.249-2.263	0.298	384	X-RAY DIFFRACTION	63	61
2.263-2.277	0.307	380	X-RAY DIFFRACTION	63	62
2.277-2.292	0.283	382	X-RAY DIFFRACTION	63	62
2.292-2.307	0.254	408	X-RAY DIFFRACTION	63	65
2.307-2.322	0.257	411	X-RAY DIFFRACTION	63	67
2.322-2.338	0.244	408	X-RAY DIFFRACTION	63	67
2.338-2.354	0.26	419	X-RAY DIFFRACTION	63	67
2.354-2.37	0.252	415	X-RAY DIFFRACTION	63	66
2.37-2.387	0.233	399	X-RAY DIFFRACTION	63	65
2.387-2.405	0.229	437	X-RAY DIFFRACTION	63	69
2.405-2.423	0.234	406	X-RAY DIFFRACTION	63	70
2.423-2.441	0.231	443	X-RAY DIFFRACTION	63	67
2.441-2.461	0.217	419	X-RAY DIFFRACTION	63	71
2.461-2.48	0.23	471	X-RAY DIFFRACTION	63	73
2.48-2.501	0.214	427	X-RAY DIFFRACTION	63	70
2.501-2.522	0.251	456	X-RAY DIFFRACTION	63	74
2.522-2.544	0.218	443	X-RAY DIFFRACTION	63	72
2.544-2.567	0.234	470	X-RAY DIFFRACTION	63	76
2.567-2.59	0.22	480	X-RAY DIFFRACTION	63	77
2.59-2.615	0.232	477	X-RAY DIFFRACTION	63	78
2.615-2.64	0.218	472	X-RAY DIFFRACTION	63	76
2.64-2.666	0.217	509	X-RAY DIFFRACTION	63	80
2.666-2.694	0.224	508	X-RAY DIFFRACTION	63	82
2.694-2.722	0.218	493	X-RAY DIFFRACTION	63	80
2.722-2.752	0.22	516	X-RAY DIFFRACTION	63	83
2.752-2.783	0.236	508	X-RAY DIFFRACTION	63	84
2.783-2.816	0.219	579	X-RAY DIFFRACTION	63	87
2.816-2.85	0.236	514	X-RAY DIFFRACTION	63	85
2.85-2.886	0.211	533	X-RAY DIFFRACTION	63	87
2.886-2.924	0.257	539	X-RAY DIFFRACTION	63	87
2.924-2.964	0.215	564	X-RAY DIFFRACTION	63	89
2.964-3.006	0.238	557	X-RAY DIFFRACTION	63	90
3.006-3.051	0.238	577	X-RAY DIFFRACTION	63	91
3.051-3.098	0.23	548	X-RAY DIFFRACTION	63	90
3.098-3.149	0.24	572	X-RAY DIFFRACTION	63	91
3.149-3.203	0.242	556	X-RAY DIFFRACTION	63	91
3.203-3.261	0.25	596	X-RAY DIFFRACTION	63	93
3.261-3.323	0.221	560	X-RAY DIFFRACTION	63	90
3.323-3.391	0.214	561	X-RAY DIFFRACTION	63	91
3.391-3.464	0.198	583	X-RAY DIFFRACTION	63	94
3.464-3.544	0.189	590	X-RAY DIFFRACTION	63	93
3.544-3.632	0.184	593	X-RAY DIFFRACTION	63	93
3.632-3.73	0.181	589	X-RAY DIFFRACTION	63	93
3.73-3.839	0.176	577	X-RAY DIFFRACTION	63	93
3.839-3.962	0.173	577	X-RAY DIFFRACTION	63	92
3.962-4.102	0.157	562	X-RAY DIFFRACTION	63	91
4.102-4.265	0.162	589	X-RAY DIFFRACTION	63	94
4.265-4.457	0.172	569	X-RAY DIFFRACTION	63	93
4.457-4.689	0.155	594	X-RAY DIFFRACTION	63	92
4.689-4.979	0.176	586	X-RAY DIFFRACTION	63	93
4.979-5.356	0.171	592	X-RAY DIFFRACTION	63	95
5.356-5.883	0.22	580	X-RAY DIFFRACTION	63	92
5.883-6.705	0.209	599	X-RAY DIFFRACTION	63	94
6.705-8.343	0.188	595	X-RAY DIFFRACTION	63	93
8.343-19.91	0.164	612	X-RAY DIFFRACTION	63	93

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