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- PDB-8fav: HUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA (RORC2) LIGAND-BINDI... -

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Basic information

Entry
Database: PDB / ID: 8fav
TitleHUMAN RETENOID-RELATED ORPHAN RECEPTOR-GAMMA (RORC2) LIGAND-BINDING DOMAIN IN COMPLEX WITH COMPOUND 5 ANDINDAZOLE ACID BOUND IN H12-POCKET
ComponentsNuclear receptor ROR-gamma
KeywordsDNA BINDING PROTEIN / RORC2 / RORgammat / structure-based design / macrocyclization / topical delivery
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / regulation of steroid metabolic process / ligand-activated 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-activated 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 / 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 / DNA-binding transcription factor activity / RNA polymerase II cis-regulatory region sequence-specific DNA binding / 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-4Y5 / Chem-LKY / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.85 Å
AuthorsVajdos, F.F.
Funding support United States, 1items
OrganizationGrant numberCountry
Other private United States
CitationJournal: Acs Med.Chem.Lett. / Year: 2023
Title: Macrocyclic Retinoic Acid Receptor-Related Orphan Receptor C2 Inverse Agonists.
Authors: Schnute, M.E. / Trujillo, J.I. / Lee, K.L. / Unwalla, R. / Vajdos, F.F. / Kauppi, B. / Nuhant, P. / Flick, A.C. / Crouse, K.K. / Zhao, Y. / Samuel, A. / Lombardo, V. / Taylor, A.P. / Brault, ...Authors: Schnute, M.E. / Trujillo, J.I. / Lee, K.L. / Unwalla, R. / Vajdos, F.F. / Kauppi, B. / Nuhant, P. / Flick, A.C. / Crouse, K.K. / Zhao, Y. / Samuel, A. / Lombardo, V. / Taylor, A.P. / Brault, A.L. / Knafels, J.D. / Vazquez, M.L. / Berstein, G.
History
DepositionNov 28, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 1, 2023Provider: repository / Type: Initial release
Revision 1.1Oct 23, 2024Group: Data collection / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature
Item: _pdbx_entry_details.has_protein_modification

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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)62,4847
Polymers60,5022
Non-polymers1,9835
Water5,224290
1
A: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,2904
Polymers30,2511
Non-polymers1,0393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,1943
Polymers30,2511
Non-polymers9432
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)47.088, 96.922, 56.914
Angle α, β, γ (deg.)90.00, 91.26, 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: 30250.811 Da / Num. of mol.: 2 / 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-LKY / 3-cyano-N-(3-{[(3S)-4-(cyclopentanecarbonyl)-3-methylpiperazin-1-yl]methyl}-5-fluoro-2-methylphenyl)benzamide


Mass: 462.559 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H31FN4O2 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-4Y5 / 4-{1-[2-chloro-6-(trifluoromethyl)benzoyl]-4-fluoro-1H-indazol-3-yl}-3-fluorobenzoic acid


Mass: 480.771 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H10ClF5N2O3
#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.: 290 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.15 Å3/Da / Density % sol: 42.69 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 100 mM MES pH 5.9, 5 mM ammonium sulfate, 300 mM magnesium chloride, 10% N,N-dimethylformamide, and 14% PEG-MME-5000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 4, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.85→96.92 Å / Num. obs: 42348 / % possible obs: 97.2 % / Redundancy: 3.4 % / CC1/2: 0.989 / Rmerge(I) obs: 0.076 / Rpim(I) all: 0.05 / Rrim(I) all: 0.092 / Net I/σ(I): 11 / Num. measured all: 142166
Reflection shellResolution: 1.85→2.07 Å / % possible obs: 97.2 % / Redundancy: 3.4 % / Rmerge(I) obs: 0.44 / Num. measured all: 41020 / Num. unique obs: 11991 / CC1/2: 0.837 / Rpim(I) all: 0.279 / Rrim(I) all: 0.523 / Net I/σ(I) obs: 3

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Processing

Software
NameVersionClassification
REFMACv5.8.0073refinement
Aimlessdata scaling
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: RORG5_IA_DIMER_P21.PDB

Resolution: 1.85→56.9 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.93 / SU B: 3.655 / SU ML: 0.112 / Cross valid method: THROUGHOUT / ESU R: 0.164 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2326 1964 4.6 %RANDOM
Rwork0.19219 ---
obs0.19414 40352 96.97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.145 Å2
Baniso -1Baniso -2Baniso -3
1-0.68 Å2-0 Å20.04 Å2
2---0.37 Å2-0 Å2
3----0.31 Å2
Refinement stepCycle: LAST / Resolution: 1.85→56.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4052 0 139 290 4481
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0194342
X-RAY DIFFRACTIONr_bond_other_d0.0080.024038
X-RAY DIFFRACTIONr_angle_refined_deg0.7041.9885875
X-RAY DIFFRACTIONr_angle_other_deg0.66239261
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.0115501
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.63222.952210
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.43715762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.1221536
X-RAY DIFFRACTIONr_chiral_restr0.0760.2619
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.024863
X-RAY DIFFRACTIONr_gen_planes_other0.0060.021053
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it2.5372.7912001
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it3.54.172503
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.7943.3682341
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.85→1.897 Å /
RfactorNum. reflection
Rfree0.351 121
Rwork0.296 2977

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