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- PDB-6bn6: IDENTIFICATION OF BICYCLIC HEXAFLUOROISOPROPYL ALCOHOL SULFONAMID... -

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Basic information

Entry
Database: PDB / ID: 6bn6
TitleIDENTIFICATION OF BICYCLIC HEXAFLUOROISOPROPYL ALCOHOL SULFONAMIDES AS RORGT/RORC INVERSE AGONISTS
ComponentsNuclear receptor ROR-gamma
KeywordsTRANSCRIPTION/TRANSCRIPTION INHIBITOR / RORGT / NUCLEAR HORMONE RECEPTOR / LIGAND-BINDING DOMAIN / INVERSE AGONIST / TRANSCRIPTION-TRANSCRIPTION INHIBITOR complex
Function / homology
Function and homology information


T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process ...T-helper 17 cell differentiation / ligand-activated transcription factor activity / cellular response to sterol / regulation of steroid metabolic process / Peyer's patch development / T-helper cell differentiation / positive regulation of circadian rhythm / oxysterol binding / RUNX3 Regulates Immune Response and Cell Migration / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / regulation of glucose metabolic process / lymph node development / adipose tissue development / xenobiotic metabolic process / circadian regulation of gene expression / DNA-binding transcription repressor activity, RNA polymerase II-specific / Nuclear Receptor transcription pathway / nuclear receptor activity / sequence-specific double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / nuclear body / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / chromatin / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / zinc ion binding / nucleoplasm / nucleus
Similarity search - Function
Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / 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 receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / 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-XGH / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.4 Å
AuthorsSack, J.
CitationJournal: Bioorg. Med. Chem. Lett. / Year: 2018
Title: Identification of bicyclic hexafluoroisopropyl alcohol sulfonamides as retinoic acid receptor-related orphan receptor gamma (ROR gamma /RORc) inverse agonists. Employing structure-based drug ...Title: Identification of bicyclic hexafluoroisopropyl alcohol sulfonamides as retinoic acid receptor-related orphan receptor gamma (ROR gamma /RORc) inverse agonists. Employing structure-based drug design to improve pregnane X receptor (PXR) selectivity.
Authors: Gong, H. / Weinstein, D.S. / Lu, Z. / Duan, J.J. / Stachura, S. / Haque, L. / Karmakar, A. / Hemagiri, H. / Raut, D.K. / Gupta, A.K. / Khan, J. / Camac, D. / Sack, J.S. / Pudzianowski, A. / ...Authors: Gong, H. / Weinstein, D.S. / Lu, Z. / Duan, J.J. / Stachura, S. / Haque, L. / Karmakar, A. / Hemagiri, H. / Raut, D.K. / Gupta, A.K. / Khan, J. / Camac, D. / Sack, J.S. / Pudzianowski, A. / Wu, D.R. / Yarde, M. / Shen, D.R. / Borowski, V. / Xie, J.H. / Sun, H. / D'Arienzo, C. / Dabros, M. / Galella, M.A. / Wang, F. / Weigelt, C.A. / Zhao, Q. / Foster, W. / Somerville, J.E. / Salter-Cid, L.M. / Barrish, J.C. / Carter, P.H. / Dhar, T.G.M.
History
DepositionNov 16, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 20, 2017Provider: repository / Type: Initial release
Revision 1.1Dec 27, 2017Group: Database references / Category: citation / citation_author
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jan 3, 2018Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.3Mar 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

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)62,9207
Polymers61,4232
Non-polymers1,4975
Water1,06359
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4123
Polymers30,7111
Non-polymers7012
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5084
Polymers30,7111
Non-polymers7973
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)99.760, 99.760, 126.550
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein Nuclear receptor ROR-gamma / Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan ...Nuclear receptor RZR-gamma / Nuclear receptor subfamily 1 group F member 3 / RAR-related orphan receptor C / Retinoid-related orphan receptor-gamma


Mass: 30711.455 Da / Num. of mol.: 2 / Fragment: Ligand-binding domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: RORC, NR1F3, RORG, RZRG / Production host: Escherichia coli (E. coli) / References: UniProt: P51449
#2: Chemical ChemComp-XGH / 2-[(2S)-4-[(4-fluorophenyl)sulfonyl]-7-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)-3,4-dihydro-2H-1,4-benzothiazin-2-yl]-N-(2-hydroxy-2-methylpropyl)acetamide


Mass: 604.558 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23F7N2O5S2
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 59 / 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: 2.96 Å3/Da / Density % sol: 58.44 %
Crystal growTemperature: 273 K / Method: vapor diffusion, hanging drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 24, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.4→46.41 Å / Num. obs: 28070 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 10.2 % / Biso Wilson estimate: 70.93 Å2 / Rmerge(I) obs: 0.039 / Net I/σ(I): 34.1
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.546 / Mean I/σ(I) obs: 3.9 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
BUSTER2.11.7refinement
RefinementResolution: 2.4→46.41 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.939 / SU R Cruickshank DPI: 0.255 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.244 / SU Rfree Blow DPI: 0.189 / SU Rfree Cruickshank DPI: 0.194
RfactorNum. reflection% reflectionSelection details
Rfree0.225 1410 5.03 %RANDOM
Rwork0.203 ---
obs0.204 28022 99.9 %-
Displacement parametersBiso mean: 66.25 Å2
Baniso -1Baniso -2Baniso -3
1--2.8518 Å20 Å20 Å2
2---2.8518 Å20 Å2
3---5.7035 Å2
Refine analyzeLuzzati coordinate error obs: 0.33 Å
Refinement stepCycle: LAST / Resolution: 2.4→46.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3529 0 93 59 3681
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013690HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.075007HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1295SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes651HARMONIC5
X-RAY DIFFRACTIONt_it3690HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.42
X-RAY DIFFRACTIONt_other_torsion19
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion466SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4192SEMIHARMONIC4
LS refinement shellResolution: 2.4→2.49 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2438 143 4.86 %
Rwork0.2295 2797 -
all0.2302 2940 -
obs--99.36 %

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