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- PDB-3kba: Progesterone receptor bound to sulfonamide pyrrolidine partial agonist -

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Basic information

Entry
Database: PDB / ID: 3kba
TitleProgesterone receptor bound to sulfonamide pyrrolidine partial agonist
ComponentsProgesterone receptor
KeywordsTRANSCRIPTION / nuclear receptor / Transcription regulation
Function / homology
Function and homology information


glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / paracrine signaling / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / progesterone receptor signaling pathway / Nuclear signaling by ERBB4 / estrogen response element binding ...glandular epithelial cell maturation / tertiary branching involved in mammary gland duct morphogenesis / ovulation from ovarian follicle / paracrine signaling / regulation of epithelial cell proliferation / nuclear steroid receptor activity / lung alveolus development / progesterone receptor signaling pathway / Nuclear signaling by ERBB4 / estrogen response element binding / intracellular steroid hormone receptor signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / G protein-coupled receptor activity / SUMOylation of intracellular receptors / transcription coactivator binding / Nuclear Receptor transcription pathway / nuclear receptor activity / cell-cell signaling / ATPase binding / DNA-binding transcription activator activity, RNA polymerase II-specific / Estrogen-dependent gene expression / mitochondrial outer membrane / nucleic acid binding / DNA-binding transcription factor activity, RNA polymerase II-specific / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of gene expression / signaling receptor binding / chromatin / positive regulation of gene expression / regulation of transcription by RNA polymerase II / enzyme binding / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / zinc ion binding / nucleoplasm / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Progesterone receptor / Progesterone receptor / 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 ...Progesterone receptor / Progesterone receptor / 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-WOW / Progesterone receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2 Å
AuthorsKallander, L.S. / Washburn, D.G. / Williams, S.P. / Madauss, K.P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2010
Title: Improving the developability profile of pyrrolidine progesterone receptor partial agonists.
Authors: Kallander, L.S. / Washburn, D.G. / Hoang, T.H. / Frazee, J.S. / Stoy, P. / Johnson, L. / Lu, Q. / Hammond, M. / Barton, L.S. / Patterson, J.R. / Azzarano, L.M. / Nagilla, R. / Madauss, K.P. ...Authors: Kallander, L.S. / Washburn, D.G. / Hoang, T.H. / Frazee, J.S. / Stoy, P. / Johnson, L. / Lu, Q. / Hammond, M. / Barton, L.S. / Patterson, J.R. / Azzarano, L.M. / Nagilla, R. / Madauss, K.P. / Williams, S.P. / Stewart, E.L. / Duraiswami, C. / Grygielko, E.T. / Xu, X. / Laping, N.J. / Bray, J.D. / Thompson, S.K.
History
DepositionOct 20, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 8, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Feb 21, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Progesterone receptor
B: Progesterone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,4135
Polymers58,5092
Non-polymers9043
Water7,656425
1
A: Progesterone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,7543
Polymers29,2541
Non-polymers5002
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Progesterone receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6582
Polymers29,2541
Non-polymers4041
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)57.394, 64.349, 70.420
Angle α, β, γ (deg.)90.000, 96.530, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Progesterone receptor / / PR / Nuclear receptor subfamily 3 group C member 3


Mass: 29254.365 Da / Num. of mol.: 2 / Fragment: Steroid-binding region: UNP residues 681-933
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PGR, NR3C3 / Production host: Escherichia coli (E. coli) / References: UniProt: P06401
#2: Chemical ChemComp-WOW / 2-chloro-4-{(2-methylbenzyl)[(3S)-1-(methylsulfonyl)pyrrolidin-3-yl]amino}benzonitrile


Mass: 403.926 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C20H22ClN3O2S
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


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


Mass: 18.015 Da / Num. of mol.: 425 / 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: 2.21 Å3/Da / Density % sol: 44.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 3350, 2mM Li2SO4, HEPES pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD
RadiationMonochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 39206 / % possible obs: 97.2 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.064 / Χ2: 0.92 / Net I/σ(I): 8.6
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
1.9-1.972.80.38733940.827184.9
1.97-2.053.10.32737620.823193.7
2.05-2.143.30.27538550.941196.1
2.14-2.253.40.20739230.945198.4
2.25-2.393.60.15540390.888199.5
2.39-2.583.80.12639930.852199.9
2.58-2.843.80.09640110.8721100
2.84-3.253.80.05940300.8741100
3.25-4.093.80.03740761.0391100
4.09-503.70.0341231.07199.8

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Phasing

PhasingMethod: molecular replacement
Phasing MRModel details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.5 Å42.68 Å
Translation2.5 Å42.68 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER1.3.3phasing
REFMACrefinement
PDB_EXTRACT3.005data extraction
StructureStudiodata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.201 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.749 / SU B: 13.851 / SU ML: 0.189 / SU R Cruickshank DPI: 0.25 / SU Rfree: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.222 / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1752 5.1 %RANDOM
Rwork0.194 ---
obs0.197 34246 98.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 76.68 Å2 / Biso mean: 34.966 Å2 / Biso min: 12.28 Å2
Baniso -1Baniso -2Baniso -3
1-3.94 Å20 Å22.26 Å2
2---1.72 Å20 Å2
3----1.71 Å2
Refinement stepCycle: LAST / Resolution: 2→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3942 0 59 425 4426
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0224188
X-RAY DIFFRACTIONr_bond_other_d0.0010.022847
X-RAY DIFFRACTIONr_angle_refined_deg0.8751.9985685
X-RAY DIFFRACTIONr_angle_other_deg0.79536997
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.5995512
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.23824.172163
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.55915775
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.5251518
X-RAY DIFFRACTIONr_chiral_restr0.0460.2649
X-RAY DIFFRACTIONr_gen_planes_refined0.0020.024509
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02819
X-RAY DIFFRACTIONr_nbd_refined0.1810.2971
X-RAY DIFFRACTIONr_nbd_other0.160.22927
X-RAY DIFFRACTIONr_nbtor_refined0.1710.22090
X-RAY DIFFRACTIONr_nbtor_other0.0840.21913
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1040.2269
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1810.223
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2420.255
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1540.229
X-RAY DIFFRACTIONr_mcbond_it0.2741.52667
X-RAY DIFFRACTIONr_mcbond_other0.041.51006
X-RAY DIFFRACTIONr_mcangle_it0.44624111
X-RAY DIFFRACTIONr_scbond_it0.64831820
X-RAY DIFFRACTIONr_scangle_it1.0224.51573
LS refinement shellResolution: 2→2.052 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.388 124 -
Rwork0.29 2291 -
all-2415 -
obs--94.82 %
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)
11.41720.28660.12872.1712-0.05251.5162-0.05450.1189-0.1114-0.16730.0784-0.09210.10630.1167-0.024-0.0852-0.00650.0613-0.1831-0.0159-0.17224.0416-10.166433.7068
20.99570.1795-0.52841.84680.39171.56550.05-0.02810.07570.0315-0.02350.0287-0.00740.0991-0.0265-0.14680.00070.0052-0.12940.0084-0.181117.2499.88571.884
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 999
2X-RAY DIFFRACTION2B1 - 999

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