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- PDB-6cn5: HUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA LIGAND- BINDING DOMA... -

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Basic information

Entry
Database: PDB / ID: 6cn5
TitleHUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA LIGAND- BINDING DOMAIN IN COMPLEX WITH INDOLE LIGAND CP9b IN INVERSE AGONIST CONFORMATION
ComponentsNuclear receptor ROR-gamma
KeywordsSIGNALING PROTEIN / ROR GAMMA / LIGAND-BINDING / NUCLEAR RECEPTOR / NON STEROIDAL / INDOLE / PFIZER / INVERSE AGONIST
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / negative regulation of thymocyte apoptotic process ...cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-modulated transcription factor activity / Peyer's patch development / positive regulation of circadian rhythm / T-helper cell differentiation / RUNX3 Regulates Immune Response and Cell Migration / oxysterol binding / negative regulation of thymocyte apoptotic process / regulation of fat cell differentiation / regulation of glucose metabolic process / adipose tissue development / lymph node development / 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 / chromatin / 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 / 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-F7M / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 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 1.3Oct 4, 2023Group: 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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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)61,4414
Polymers60,5022
Non-polymers9392
Water1,802100
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7202
Polymers30,2511
Non-polymers4701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,7202
Polymers30,2511
Non-polymers4701
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)95.663, 95.663, 135.897
Angle α, β, γ (deg.)90.000, 90.000, 120.000
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: 30250.900 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-F7M / 4-cyano-N-{3-[1-(cyclohexanecarbonyl)piperidin-4-yl]-1-methyl-1H-indol-5-yl}pyridine-2-carboxamide


Mass: 469.578 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H31N5O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 100 / 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: 2.8 Å3/Da / Density % sol: 56 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.5
Details: 1.8-2.5M Na formate, 0.1 MTris-HCl pH 7.5-8.0, 3% methyl pentane diol

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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 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.55→135.9 Å / Num. obs: 31330 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 10.33 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 8.93
Reflection shellResolution: 2.3→2.42 Å / Redundancy: 10.23 % / Rmerge(I) obs: 0.54 / Mean I/σ(I) obs: 1.43 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.5.0109refinement
PDB_EXTRACT3.24data extraction
XDSdata reduction
autoPROCdata scaling
REFMACphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B0W
Resolution: 2.3→82.85 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.936 / SU B: 10.96 / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.214 / ESU R Free: 0.19
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES AFTER 495 ARE DISORDERED
RfactorNum. reflection% reflectionSelection details
Rfree0.2222 1575 5 %RANDOM
Rwork0.1709 ---
obs0.1735 29699 99.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å
Displacement parametersBiso max: 60.4 Å2 / Biso mean: 27.78 Å2 / Biso min: 12.21 Å2
Baniso -1Baniso -2Baniso -3
1-1.04 Å20.52 Å20 Å2
2--1.04 Å20 Å2
3----1.56 Å2
Refinement stepCycle: final / Resolution: 2.3→82.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3776 0 70 100 3946
Biso mean--28.66 29.56 -
Num. residues----462
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONBOND LENGTHS REFINED (A)0.0230.0213942
X-RAY DIFFRACTIONBOND LENGTHS OTHERS (A)
X-RAY DIFFRACTIONBOND ANGLES REFINED (DEGREES)2.0211.9675312
X-RAY DIFFRACTIONBOND ANGLES OTHERS (DEGREES)
X-RAY DIFFRACTIONTORSION ANGLES, PERIOD 1 (DEGREES)5.6475462
X-RAY DIFFRACTIONTORSION ANGLES, PERIOD 2 (DEGREES)
X-RAY DIFFRACTIONTORSION ANGLES, PERIOD 3 (DEGREES)19.98715721
X-RAY DIFFRACTIONTORSION ANGLES, PERIOD 4 (DEGREES)
X-RAY DIFFRACTIONCHIRAL-CENTER RESTRAINTS (A**3)0.1480.2577
X-RAY DIFFRACTIONGENERAL PLANES REFINED (A)0.0090.022970
X-RAY DIFFRACTIONGENERAL PLANES OTHERS (A)
X-RAY DIFFRACTIONNON-BONDED CONTACTS REFINED (A)
X-RAY DIFFRACTIONNON-BONDED CONTACTS OTHERS (A)
X-RAY DIFFRACTIONNON-BONDED TORSION REFINED (A)
X-RAY DIFFRACTIONNON-BONDED TORSION OTHERS (A)
X-RAY DIFFRACTIONH-BOND (X...Y) REFINED (A)
X-RAY DIFFRACTIONSYMMETRY VDW REFINED (A)
X-RAY DIFFRACTIONSYMMETRY VDW OTHERS (A)
X-RAY DIFFRACTIONSYMMETRY H-BOND REFINED (A)
LS refinement shellResolution: 2.3→2.36 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection
Rfree0.255 123
Rwork0.172 2169
all-2292

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