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- PDB-6cn6: RORC2 LBD complexed with compound 34 -

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Basic information

Entry
Database: PDB / ID: 6cn6
TitleRORC2 LBD complexed with compound 34
ComponentsNuclear receptor ROR-gamma
KeywordsSIGNALING PROTEIN / Nuclear receptor
Function / homology
Function and homology information


tolerance induction in gut-associated lymphoid tissue / T-helper 17 cell differentiation / cellular response to sterol / regulation of steroid metabolic process / ligand-modulated transcription factor activity / Peyer's patch development / regulatory T cell differentiation / positive regulation of circadian rhythm / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration ...tolerance induction in gut-associated lymphoid tissue / T-helper 17 cell differentiation / cellular response to sterol / regulation of steroid metabolic process / ligand-modulated transcription factor activity / Peyer's patch development / regulatory T cell differentiation / positive regulation of circadian rhythm / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / negative regulation of thymocyte apoptotic process / Phosphorylated BMAL1:CLOCK (ARNTL:CLOCK) activates expression of core clock genes / regulation of fat cell differentiation / regulation of glucose metabolic process / adipose tissue development / lymph node development / RORA,B,C and NR1D1 (REV-ERBA) regulate gene expression / Expression of BMAL (ARNTL), CLOCK, and NPAS2 / xenobiotic metabolic process / circadian regulation of gene expression / Nuclear Receptor transcription pathway / DNA-binding transcription repressor activity, RNA polymerase II-specific / nuclear receptor activity / sequence-specific double-stranded DNA binding / Interleukin-4 and Interleukin-13 signaling / DNA-binding transcription factor activity, RNA polymerase II-specific / nuclear body / RNA polymerase II cis-regulatory region sequence-specific DNA binding / DNA-binding transcription factor activity / regulation of transcription by RNA polymerase II / positive regulation of DNA-templated transcription / chromatin / 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 / Double treble clef zinc finger, C4 type / 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 / Double treble clef zinc finger, C4 type / 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-F7J / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.45 Å
AuthorsKauppi, B. / Vajdos, F.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Discovery of 3-Cyano- N-(3-(1-isobutyrylpiperidin-4-yl)-1-methyl-4-(trifluoromethyl)-1 H-pyrrolo[2,3- b]pyridin-5-yl)benzamide: A Potent, Selective, and Orally Bioavailable Retinoic Acid ...Title: Discovery of 3-Cyano- N-(3-(1-isobutyrylpiperidin-4-yl)-1-methyl-4-(trifluoromethyl)-1 H-pyrrolo[2,3- b]pyridin-5-yl)benzamide: A Potent, Selective, and Orally Bioavailable Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonist.
Authors: Schnute, M.E. / Wennerstal, M. / Alley, J. / Bengtsson, M. / Blinn, J.R. / Bolten, C.W. / Braden, T. / Bonn, T. / Carlsson, B. / Caspers, N. / Chen, M. / Choi, C. / Collis, L.P. / Crouse, K. ...Authors: Schnute, M.E. / Wennerstal, M. / Alley, J. / Bengtsson, M. / Blinn, J.R. / Bolten, C.W. / Braden, T. / Bonn, T. / Carlsson, B. / Caspers, N. / Chen, M. / Choi, C. / Collis, L.P. / Crouse, K. / Farnegardh, M. / Fennell, K.F. / Fish, S. / Flick, A.C. / Goos-Nilsson, A. / Gullberg, H. / Harris, P.K. / Heasley, S.E. / Hegen, M. / Hromockyj, A.E. / Hu, X. / Husman, B. / Janosik, T. / Jones, P. / Kaila, N. / Kallin, E. / Kauppi, B. / Kiefer, J.R. / Knafels, J. / Koehler, K. / Kruger, L. / Kurumbail, R.G. / Kyne Jr., R.E. / Li, W. / Lofstedt, J. / Long, S.A. / Menard, C.A. / Mente, S. / Messing, D. / Meyers, M.J. / Napierata, L. / Noteberg, D. / Nuhant, P. / Pelc, M.J. / Prinsen, M.J. / Rhonnstad, P. / Backstrom-Rydin, E. / Sandberg, J. / Sandstrom, M. / Shah, F. / Sjoberg, M. / Sundell, A. / Taylor, A.P. / Thorarensen, A. / Trujillo, J.I. / Trzupek, J.D. / Unwalla, R. / Vajdos, F.F. / Weinberg, R.A. / Wood, D.C. / Xing, L. / Zamaratski, E. / Zapf, C.W. / Zhao, Y. / Wilhelmsson, A. / Berstein, G.
History
DepositionMar 7, 2018Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.title / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2May 1, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Mar 6, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name
Revision 1.4Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,4042
Polymers29,9351
Non-polymers4691
Water1,63991
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)90.840, 90.840, 138.252
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122

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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: 29935.422 Da / Num. of mol.: 1 / Fragment: ligand binding domain / Mutation: C278S, C345S
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-F7J / 3-cyano-N-{3-[1-(cyclopentanecarbonyl)piperidin-4-yl]-1,4-dimethyl-1H-indol-5-yl}benzamide


Mass: 468.590 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H32N4O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 91 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.75 Å3/Da / Density % sol: 55.28 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 8.7 / Details: 0.1 M Tris pH 8.7, 27% ethanol

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 24, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.45→138.25 Å / Num. obs: 243204 / % possible obs: 100 % / Redundancy: 18.6 % / Net I/σ(I): 20.5
Reflection shellResolution: 2.45→3 Å

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
autoPROCdata scaling
REFMACphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2.45→78.67 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.9301 / SU R Cruickshank DPI: 0.3 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.33 / SU Rfree Blow DPI: 0.238 / SU Rfree Cruickshank DPI: 0.232
RfactorNum. reflection% reflectionSelection details
Rfree0.2407 664 5.12 %RANDOM
Rwork0.1888 ---
obs0.1917 12980 99.95 %-
Displacement parametersBiso max: 156.29 Å2 / Biso mean: 66.29 Å2 / Biso min: 29.25 Å2
Baniso -1Baniso -2Baniso -3
1-5.9551 Å20 Å20 Å2
2--5.9551 Å20 Å2
3----11.9102 Å2
Refine analyzeLuzzati coordinate error obs: 0.297 Å
Refinement stepCycle: final / Resolution: 2.45→78.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1879 0 35 91 2005
Biso mean--48.71 70.7 -
Num. residues----230
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d731SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes46HARMONIC2
X-RAY DIFFRACTIONt_gen_planes322HARMONIC5
X-RAY DIFFRACTIONt_it2005HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion241SEMIHARMONIC5
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_contact2300SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d2005HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg2736HARMONIC21.02
X-RAY DIFFRACTIONt_omega_torsion2.48
X-RAY DIFFRACTIONt_other_torsion18.84
LS refinement shellResolution: 2.45→2.65 Å / Rfactor Rfree error: 0 / Total num. of bins used: 7
RfactorNum. reflection% reflection
Rfree0.2622 108 4.17 %
Rwork0.2177 2483 -
all0.2195 2591 -
obs--100 %

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