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- PDB-9n9l: An RORgt Inverse agonist for treatment of Psoriasis -

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Basic information

Entry
Database: PDB / ID: 9n9l
TitleAn RORgt Inverse agonist for treatment of Psoriasis
ComponentsNuclear receptor ROR-gamma
KeywordsNUCLEAR PROTEIN / Nuclear Hormone Receptor
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 / 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 ...Nuclear receptor ROR / Retinoid-related orphan receptors, DNA-binding domain / 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
Similarity search - Domain/homology
: / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.637 Å
AuthorsSpurlino, J.C. / Milligan, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2025
Title: Identification of JNJ-61803534, a ROR gamma t Inverse Agonist for the Treatment of Psoriasis.
Authors: Kinzel, O. / Goldberg, S.D. / Cummings, M.D. / Gege, C. / Steeneck, C. / Xue, X. / Albers, M. / Schluter, T. / Kleymann, G. / Scott, B. / Sepassi, K. / Schoetens, F. / Venkatesan, H. / ...Authors: Kinzel, O. / Goldberg, S.D. / Cummings, M.D. / Gege, C. / Steeneck, C. / Xue, X. / Albers, M. / Schluter, T. / Kleymann, G. / Scott, B. / Sepassi, K. / Schoetens, F. / Venkatesan, H. / Tanis, V.M. / Coe, K. / Sales, Z.S. / Spurlino, J. / Milligan, C. / Fourie, A.M. / Edwards, J.P. / Hoffmann, T.
History
DepositionFeb 11, 2025Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 30, 2025Provider: repository / Type: Initial release
Revision 1.1May 7, 2025Group: 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

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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)57,8604
Polymers56,6162
Non-polymers1,2452
Water2,810156
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9302
Polymers28,3081
Non-polymers6221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,9302
Polymers28,3081
Non-polymers6221
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.503, 128.898, 51.832
Angle α, β, γ (deg.)90.00, 91.38, 90.00
Int Tables number4
Space group name H-MP1211

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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: 28307.824 Da / Num. of mol.: 2
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-A1BW2 / (5P)-5-[2,3-dichloro-4-(1,1,1,3,3,3-hexafluoro-2-hydroxypropan-2-yl)phenyl]-N-(2-hydroxy-2-methylpropyl)-4-[(2S)-2-methylpyrrolidine-1-carbonyl]-1,3-thiazole-2-carboxamide


Mass: 622.408 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C23H23Cl2F6N3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 156 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 2.45 Å3/Da / Density % sol: 49.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 18% PEG 4000, 0.1 M Hepes pH 7.5 and 0.1 M Ammonium Acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: May 16, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.637→40.383 Å / Num. obs: 66034 / % possible obs: 98.81 % / Redundancy: 3.8 % / Biso Wilson estimate: 23.12 Å2 / Rmerge(I) obs: 0.052 / Net I/σ(I): 22.2
Reflection shellResolution: 1.637→1.696 Å / Rmerge(I) obs: 0.509 / Num. unique obs: 6394 / % possible all: 96.13

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Processing

Software
NameVersionClassification
PHENIXdev-2026_1692refinement
HKL-2000data scaling
HKL-2000data reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.637→40.383 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 23.49 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2248 1998 3.03 %
Rwork0.1908 --
obs0.1919 66024 98.77 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.637→40.383 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3730 0 78 156 3964
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0143900
X-RAY DIFFRACTIONf_angle_d1.4835269
X-RAY DIFFRACTIONf_dihedral_angle_d14.991451
X-RAY DIFFRACTIONf_chiral_restr0.067563
X-RAY DIFFRACTIONf_plane_restr0.007675
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.637-1.67760.27381350.24774392X-RAY DIFFRACTION95
1.6776-1.7230.26871420.22384563X-RAY DIFFRACTION98
1.723-1.77370.24421390.20684502X-RAY DIFFRACTION99
1.7737-1.83090.2451430.19864568X-RAY DIFFRACTION99
1.8309-1.89640.22021480.19534567X-RAY DIFFRACTION99
1.8964-1.97230.23091440.2044617X-RAY DIFFRACTION99
1.9723-2.06210.24971390.19914568X-RAY DIFFRACTION99
2.0621-2.17080.20341370.18874593X-RAY DIFFRACTION99
2.1708-2.30680.24081460.1814585X-RAY DIFFRACTION99
2.3068-2.48480.22381470.19814583X-RAY DIFFRACTION99
2.4848-2.73490.23231490.20634627X-RAY DIFFRACTION100
2.7349-3.13050.26621370.2064604X-RAY DIFFRACTION100
3.1305-3.94350.23391500.18564633X-RAY DIFFRACTION100
3.9435-100.17731420.16974624X-RAY DIFFRACTION98
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.83352.4142-2.93883.9547-3.44234.9491-0.1890.2971-0.0259-0.56310.5270.4310.4816-0.6757-0.42130.2859-0.0346-0.08060.28790.08470.2861-14.09231.988767.8543
20.8250.1056-0.1530.9470.18160.6186-0.04780.10830.0613-0.07550.0975-0.05750.11070.0334-0.04980.1951-0.0068-0.01960.19140.00290.19267.604815.00454.5399
32.3387-1.1183-1.25393.06840.872.50080.0699-0.09270.00270.09630.01550.1696-0.0994-0.0721-0.08760.1831-0.0132-0.00010.20740.03770.1839-6.382216.715369.0297
41.7470.0703-1.04671.1037-0.42420.7001-0.0425-0.2565-0.12090.1014-0.0003-0.19420.11940.11550.04390.2251-0.0011-0.05490.23210.02790.22710.36929.65364.1166
51.3561-0.3323-0.7323.4154-0.17661.4285-0.1176-0.2547-0.19440.46670.15390.2485-0.01-0.1007-0.04290.25440.0008-0.02350.28590.0710.2297-7.94236.74678.4565
60.82470.3308-0.14260.92330.23070.12850.0646-0.31270.14870.11060.0349-0.0449-0.47760.13260.12461.13910.160.13930.4917-0.09760.10197.705112.230677.6884
72.0080.6622-0.53334.7199-1.35731.8754-0.0222-0.24330.23390.42240.0110.1284-0.23560.03520.02820.25750.0123-0.02550.2528-0.0320.28969.466928.914365.5228
82.8798-1.60971.99273.6008-2.59183.5464-0.2455-0.36110.18230.67580.5220.6161-0.4469-0.7867-0.19820.36070.06210.1080.34790.06580.3339-15.9686-5.056744.0527
94.92821.98911.95422.99560.56713.22410.1403-0.57990.44960.8401-0.20070.49840.1483-0.2193-0.13650.47670.02280.03720.2559-0.0540.31152.6768-9.401456.6704
101.0003-0.10070.17775.44771.74552.0196-0.0454-0.27450.01890.714-0.0345-0.33650.01480.1321-0.02540.26830.014-0.06920.3097-0.02310.242919.0135-23.96957.0993
114.2622-2.0081.35291.979-0.83871.3983-0.0916-0.3298-0.13650.1680.19760.1199-0.0689-0.0656-0.04860.2015-0.00880.01320.1973-0.00950.2016-0.219-26.109948.5488
122.2089-0.00821.56511.1548-0.09141.8535-0.01880.04370.2069-0.0027-0.01130.0751-0.0508-0.07440.01290.18830.01590.02550.20030.00330.19-1.2348-17.150243.2544
131.8761-0.91130.97363.0253-0.98081.1873-0.01650.2430.0805-0.2274-0.0058-0.3633-0.08440.16240.07260.214-0.02150.04420.2479-0.00540.252313.4771-17.431242.9494
142.02071.04541.26793.14741.47512.990.01070.16260.09990.0840.06170.10080.11040.0394-0.12940.24820.0270.00130.21620.05130.2349-6.8176-11.921335.9611
152.18131.20521.3954.20831.28832.9333-0.03610.13380.1948-0.23540.06840.3077-0.1803-0.20820.00080.21310.00810.00410.24650.09740.2536-13.1062-5.228532.2961
164.1335-1.12730.01733.83361.51313.49920.01340.71880.5386-0.47590.1244-0.49620.37030.2014-0.08010.45750.01950.1040.31720.07120.28330.522-0.896935.527
172.659-0.0781-0.11785.19180.36270.9889-0.03640.2297-0.2283-0.59470.0740.2385-0.32260.01390.06320.3544-0.00540.00330.3261-0.08460.24047.0945-29.184637.5334
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 265 through 284 )
2X-RAY DIFFRACTION2chain 'A' and (resid 285 through 337 )
3X-RAY DIFFRACTION3chain 'A' and (resid 338 through 368 )
4X-RAY DIFFRACTION4chain 'A' and (resid 369 through 425 )
5X-RAY DIFFRACTION5chain 'A' and (resid 426 through 465 )
6X-RAY DIFFRACTION6chain 'A' and (resid 466 through 474 )
7X-RAY DIFFRACTION7chain 'A' and (resid 475 through 492 )
8X-RAY DIFFRACTION8chain 'B' and (resid 265 through 284 )
9X-RAY DIFFRACTION9chain 'B' and (resid 285 through 297 )
10X-RAY DIFFRACTION10chain 'B' and (resid 298 through 312 )
11X-RAY DIFFRACTION11chain 'B' and (resid 313 through 337 )
12X-RAY DIFFRACTION12chain 'B' and (resid 338 through 384 )
13X-RAY DIFFRACTION13chain 'B' and (resid 385 through 410 )
14X-RAY DIFFRACTION14chain 'B' and (resid 411 through 435 )
15X-RAY DIFFRACTION15chain 'B' and (resid 436 through 456 )
16X-RAY DIFFRACTION16chain 'B' and (resid 457 through 470 )
17X-RAY DIFFRACTION17chain 'B' and (resid 471 through 492 )

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