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- PDB-3vhv: Mineralocorticoid receptor ligand-binding domain with non-steroid... -

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Basic information

Entry
Database: PDB / ID: 3vhv
TitleMineralocorticoid receptor ligand-binding domain with non-steroidal antagonist
ComponentsMineralocorticoid receptor
KeywordsTRANSCRIPTION/INHIBITOR / NUCLEAR RECEPTOR / TRANSCRIPTION FACTOR / ACTIVATING MUTATION / HYPERTENSION / NON-STEROIDAL ANTAGONIST / TRANSCRIPTION-INHIBITOR complex
Function / homology
Function and homology information


nuclear steroid receptor activity / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / TBP-class protein binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / positive regulation of non-canonical NF-kappaB signal transduction / nuclear receptor activity ...nuclear steroid receptor activity / estrogen response element binding / nuclear receptor-mediated steroid hormone signaling pathway / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / steroid binding / TBP-class protein binding / SUMOylation of intracellular receptors / Nuclear Receptor transcription pathway / positive regulation of non-canonical NF-kappaB signal transduction / nuclear receptor activity / sequence-specific double-stranded DNA binding / receptor complex / DNA-binding transcription factor activity, RNA polymerase II-specific / DNA-binding transcription factor activity / endoplasmic reticulum membrane / chromatin / regulation of transcription by RNA polymerase II / signal transduction / zinc ion binding / nucleoplasm / cytosol
Similarity search - Function
: / Retinoid X Receptor / Retinoid X 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 ...: / Retinoid X Receptor / Retinoid X 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-LD1 / Chem-LD2 / Mineralocorticoid receptor
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsSogabe, S. / Habuka, N.
CitationJournal: J.Med.Chem. / Year: 2011
Title: Identification of Benzoxazin-3-one Derivatives as Novel, Potent, and Selective Nonsteroidal Mineralocorticoid Receptor Antagonists
Authors: Hasui, T. / Matsunaga, N. / Ora, T. / Ohyabu, N. / Nishigaki, N. / Imura, Y. / Igata, Y. / Matsui, H. / Motoyaji, T. / Tanaka, T. / Habuka, N. / Sogabe, S. / Ono, M. / Siedem, C.S. / Tang, T. ...Authors: Hasui, T. / Matsunaga, N. / Ora, T. / Ohyabu, N. / Nishigaki, N. / Imura, Y. / Igata, Y. / Matsui, H. / Motoyaji, T. / Tanaka, T. / Habuka, N. / Sogabe, S. / Ono, M. / Siedem, C.S. / Tang, T.P. / Gauthier, C. / De Meese, L.A. / Boyd, S.A. / Fukumoto, S.
History
DepositionSep 7, 2011Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _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: Mineralocorticoid receptor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,0526
Polymers30,1601
Non-polymers8925
Water4,864270
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)62.612, 62.612, 75.504
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number145
Space group name H-MP32

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mineralocorticoid receptor / MR / Nuclear receptor subfamily 3 group C member 2


Mass: 30159.953 Da / Num. of mol.: 1 / Fragment: LIGAND-BINDING DOMAIN, UNP residues 727-984 / Mutation: C808S, S810L, A976V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NR3C2, MCR, MLR / Production host: Escherichia coli (E. coli) / References: UniProt: P08235

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Non-polymers , 5 types, 275 molecules

#2: Chemical ChemComp-LD1 / 6-[(7S)-7-phenyl-7H-[1,2,4]triazolo[3,4-b][1,3,4]thiadiazin-6-yl]-2H-1,4-benzoxazin-3(4H)-one


Mass: 363.393 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13N5O2S
#3: Chemical ChemComp-LD2 / 6-[(1E)-2-phenyl-N-(3-sulfanyl-4H-1,2,4-triazol-4-yl)ethanimidoyl]-2H-1,4-benzoxazin-3(4H)-one / 6-[(1E)-N-(3-mercapto-4H-1,2,4-triazolo-4-yl)-2-phenylethanimidoyl]-2H-1,4-benzooxazin-3(4H)-one


Mass: 365.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H15N5O2S
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-K / POTASSIUM ION


Mass: 39.098 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: K
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 270 / 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: 2.83 Å3/Da / Density % sol: 56.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.1M HEPES pH 7.4, 0.88M potassium/sodium tartrate, 5% ethylene glycol, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210r / Detector: CCD / Date: Feb 17, 2007
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.35→50 Å / Num. obs: 71863 / % possible obs: 98.6 % / Observed criterion σ(I): 1 / Redundancy: 3.7 % / Rsym value: 0.045 / Net I/σ(I): 22.5
Reflection shellResolution: 1.35→1.4 Å / Redundancy: 2.5 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.41 / % possible all: 88.4

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Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2AB2

2ab2


Resolution: 1.35→40 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.97 / SU B: 1.178 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.16735 3608 5 %RANDOM
Rwork0.14116 ---
obs0.14247 68224 98.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.473 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å2-0.14 Å20 Å2
2---0.29 Å20 Å2
3---0.43 Å2
Refinement stepCycle: LAST / Resolution: 1.35→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2084 0 61 270 2415
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0222283
X-RAY DIFFRACTIONr_angle_refined_deg1.2432.0033101
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.1955277
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04324.412102
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.85215428
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.5611511
X-RAY DIFFRACTIONr_chiral_restr0.0710.2339
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0211787
X-RAY DIFFRACTIONr_mcbond_it2.29521313
X-RAY DIFFRACTIONr_mcangle_it3.54732149
X-RAY DIFFRACTIONr_scbond_it4.924970
X-RAY DIFFRACTIONr_scangle_it7.0346940
X-RAY DIFFRACTIONr_rigid_bond_restr2.03832283
LS refinement shellResolution: 1.349→1.384 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.343 216 -
Rwork0.316 4384 -
obs--85.44 %

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