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- PDB-7jtw: Crystal structure of RORgt with compound (4R)-6-[(2,5-dichloro-3-... -

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Basic information

Entry
Database: PDB / ID: 7jtw
TitleCrystal structure of RORgt with compound (4R)-6-[(2,5-dichloro-3-{[(2R,4R)-1-(cyclopentanecarbonyl)-2-methylpiperidin-4-yl]oxy}phenyl)amino]-6-oxo-4-phenylhexanoic acid
ComponentsRAR-related orphan receptor C isoform a variant
KeywordsNUCLEAR PROTEIN / nuclear receptor
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 / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / 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 / positive regulation of circadian rhythm / oxysterol binding / T-helper cell differentiation / 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 / sequence-specific DNA binding / 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 / 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 ...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 / 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
Similarity search - Domain/homology
Chem-VK4 / Nuclear receptor ROR-gamma / RAR-related orphan receptor C isoform a variant
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsMin, X. / Wang, Z.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2021
Title: Discovery of 6-Oxo-4-phenyl-hexanoic acid derivatives as ROR gamma t inverse agonists showing favorable ADME profile.
Authors: Nakajima, R. / Oono, H. / Kumazawa, K. / Ida, T. / Hirata, J. / White, R.D. / Min, X. / Guzman-Perez, A. / Wang, Z. / Symons, A. / Singh, S.K. / Mothe, S.R. / Belyakov, S. / Chakrabarti, A. / Shuto, S.
History
DepositionAug 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 3, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 10, 2021Group: Database references / Category: citation
Item: _citation.page_first / _citation.page_last ..._citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title
Revision 1.2Feb 17, 2021Group: Database references / Category: citation / Item: _citation.journal_volume / _citation.title
Revision 1.3Oct 18, 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
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: RAR-related orphan receptor C isoform a variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)32,1506
Polymers31,2021
Non-polymers9485
Water2,036113
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area990 Å2
ΔGint-19 kcal/mol
Surface area12180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.991, 61.991, 156.838
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein RAR-related orphan receptor C isoform a variant / RORgt / RORc


Mass: 31202.025 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human)
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q53FZ4, UniProt: P51449*PLUS
#2: Chemical ChemComp-VK4 / (4R)-6-[(2,5-dichloro-3-{[(2R,4R)-1-(cyclopentanecarbonyl)-2-methylpiperidin-4-yl]oxy}phenyl)amino]-6-oxo-4-phenylhexanoic acid


Mass: 575.523 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H36Cl2N2O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20% PEG3350, 100 mM sodium citrate, pH 5

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Data collection

DiffractionMean temperature: 80 K / Ambient temp details: LN2 cryo / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 12, 2016
RadiationMonochromator: Liquid Nitrogen cooled Dual Crystal Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→29.22 Å / Num. obs: 25043 / % possible obs: 100 % / Redundancy: 12.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.143 / Net I/σ(I): 14.8 / Num. measured all: 319741
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. measured allNum. unique obsCC1/2Net I/σ(I) obs% possible all
1.9-1.9412.71.6552075316370.6471.9100
8.91-29.2210.40.04431473030.9994597.8

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Processing

Software
NameVersionClassification
PHENIXv1.18.2refinement
XDSdata reduction
Aimless0.5.15data scaling
PDB_EXTRACT3.25data extraction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 6O3Z

6o3z


Resolution: 1.9→29.22 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.3 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2331 1303 5.22 %RANDOM
Rwork0.1975 23665 --
obs0.1994 24968 99.99 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 74.19 Å2 / Biso mean: 28.7441 Å2 / Biso min: 14.92 Å2
Refinement stepCycle: final / Resolution: 1.9→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2109 0 62 113 2284
Biso mean--29.46 34.69 -
Num. residues----259
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 9 / % reflection obs: 100 %

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all
1.9-1.980.33881570.267425542711
1.98-2.070.27961420.227225782720
2.07-2.170.24851520.202925472699
2.18-2.310.23661470.189926012748
2.31-2.490.22961180.190826092727
2.49-2.740.25221340.202726232757
2.74-3.140.2751190.210826722791
3.14-3.950.20731570.183126622819
3.95-29.220.20651770.188428192996

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