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- PDB-6xae: SUBSTITUTED BENZYLOXYTRICYCLIC COMPOUNDS AS RETINOIC ACID-RELATED... -

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Basic information

Entry
Database: PDB / ID: 6xae
TitleSUBSTITUTED BENZYLOXYTRICYCLIC COMPOUNDS AS RETINOIC ACID-RELATED ORPHAN RECEPTOR GAMMA T AGONISTS
ComponentsNuclear receptor ROR-gamma
KeywordsTRANSFERASE/TRANSFERASE INHIBITOR / RORGT / NUCLEAR HORMONE RECEPTOR / LIGAND-BINDING DOMAIN / INVE AGONIST / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX / TRANSFERASE
Function / homology
Function and homology information


cellular response to sterol / T-helper 17 cell differentiation / ligand-activated transcription factor activity / regulation of steroid metabolic process / 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 / ligand-activated transcription factor activity / regulation of steroid metabolic process / 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 / Retinoid X Receptor / Retinoid X Receptor / 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 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 / 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 / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Chem-Z7F / Nuclear receptor ROR-gamma
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.257 Å
AuthorsSack, J.S.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2020
Title: Substituted benzyloxytricyclic compounds as retinoic acid-related orphan receptor gamma t (ROR gamma t) agonists.
Authors: Harikrishnan, L.S. / Gill, P. / Kamau, M.G. / Qin, L.Y. / Ruan, Z. / O'Malley, D. / Huynh, T. / Stachura, S. / Cavallaro, C.L. / Lu, Z. / J-W Duan, J. / Weigelt, C.A. / Sack, J.S. / Ruzanov, ...Authors: Harikrishnan, L.S. / Gill, P. / Kamau, M.G. / Qin, L.Y. / Ruan, Z. / O'Malley, D. / Huynh, T. / Stachura, S. / Cavallaro, C.L. / Lu, Z. / J-W Duan, J. / Weigelt, C.A. / Sack, J.S. / Ruzanov, M. / Khan, J. / Gururajan, M. / Wong, J.J. / Huang, Y. / Yarde, M. / Li, Z. / Chen, C. / Sun, H. / Borowski, V. / Murtaza, A. / Fink, B.E.
History
DepositionJun 4, 2020Deposition site: RCSB / Processing site: RCSB
SupersessionJun 17, 2020ID: 6W9J
Revision 1.0Jun 17, 2020Provider: repository / Type: Initial release
Revision 1.1Jun 24, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_id_CSD / _citation.journal_volume ..._citation.journal_id_CSD / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.title / _citation_author.name
Revision 1.2Oct 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: Nuclear receptor ROR-gamma
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,5312
Polymers32,8871
Non-polymers6441
Water36020
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area12380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.236, 62.236, 156.811
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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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: 32886.922 Da / Num. of mol.: 1
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-Z7F / trans-4-{(3aR,9bR)-7-[(2-chloro-6-fluorophenyl)methoxy]-9b-[(4-fluorophenyl)sulfonyl]-1,2,3a,4,5,9b-hexahydro-3H-benzo[e]indole-3-carbonyl}cyclohexane-1-carboxylic acid


Mass: 644.125 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H32ClF2NO6S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 20 / 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: 2.26 Å3/Da / Density % sol: 45.48 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: PROTEIN AT 8-10MG/ML, WITH 0.2M MGCL2, 22% PEG3350, 0.1M BIS-TRIS PH 5.5, PH 0, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 0.98 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Aug 31, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.257→78.4 Å / Num. obs: 8048 / % possible obs: 96.4 % / Observed criterion σ(I): 0 / Redundancy: 7.6 % / Biso Wilson estimate: 39.33 Å2 / Rmerge(I) obs: 0.204 / Net I/σ(I): 10.8
Reflection shellResolution: 2.93→3.09 Å / Redundancy: 8 % / Rmerge(I) obs: 1.078 / Mean I/σ(I) obs: 2.2 / Num. unique obs: 1006 / % possible all: 100

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
BUSTER2.11.7 (6-FEB-2020)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6vqf

6vqf


Resolution: 2.257→57.85 Å / Cor.coef. Fo:Fc: 0.91 / Cor.coef. Fo:Fc free: 0.862 / Cross valid method: THROUGHOUT / σ(F): 0 / SU Rfree Blow DPI: 0.379
RfactorNum. reflection% reflectionSelection details
Rfree0.265 409 5.08 %RANDOM
Rwork0.2078 ---
obs0.2106 8048 52.8 %-
Displacement parametersBiso mean: 34.94 Å2
Baniso -1Baniso -2Baniso -3
1-0.0337 Å20 Å20 Å2
2--0.0337 Å20 Å2
3----0.0673 Å2
Refine analyzeLuzzati coordinate error obs: 0.42 Å
Refinement stepCycle: LAST / Resolution: 2.257→57.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2054 0 44 20 2118
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0082178HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.912973HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d779SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes395HARMONIC5
X-RAY DIFFRACTIONt_it2146HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.54
X-RAY DIFFRACTIONt_other_torsion18.99
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion263SEMIHARMONIC5
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_contact1729SEMIHARMONIC4
LS refinement shellResolution: 2.26→2.56 Å
RfactorNum. reflection% reflection
Rfree0.3566 -4.71 %
Rwork0.2414 384 -

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