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- PDB-6tfi: PXR IN COMPLEX WITH THROMBIN INHIBITOR COMPOUND 17 -

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Basic information

Entry
Database: PDB / ID: 6tfi
TitlePXR IN COMPLEX WITH THROMBIN INHIBITOR COMPOUND 17
ComponentsNuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1
KeywordsTRANSCRIPTION / PXR / SRC-1 / CYP3A4 INDUCTION / PK OPTIMIZATION
Function / homology
Function and homology information


cellular response to molecule of bacterial origin / intestinal epithelial structure maintenance / intermediate filament cytoskeleton / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / xenobiotic transport / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / male mating behavior ...cellular response to molecule of bacterial origin / intestinal epithelial structure maintenance / intermediate filament cytoskeleton / labyrinthine layer morphogenesis / positive regulation of transcription from RNA polymerase II promoter by galactose / regulation of thyroid hormone receptor signaling pathway / positive regulation of female receptivity / xenobiotic transport / NR1H2 & NR1H3 regulate gene expression to control bile acid homeostasis / male mating behavior / hypothalamus development / steroid metabolic process / cellular response to Thyroglobulin triiodothyronine / Synthesis of bile acids and bile salts / progesterone receptor signaling pathway / Synthesis of bile acids and bile salts via 27-hydroxycholesterol / Endogenous sterols / Synthesis of bile acids and bile salts via 7alpha-hydroxycholesterol / response to retinoic acid / xenobiotic catabolic process / estrous cycle / nuclear retinoid X receptor binding / histone acetyltransferase activity / cellular response to hormone stimulus / Recycling of bile acids and salts / Transcriptional regulation of brown and beige adipocyte differentiation by EBF2 / histone acetyltransferase / NR1H3 & NR1H2 regulate gene expression linked to cholesterol transport and efflux / intracellular receptor signaling pathway / estrogen receptor signaling pathway / lactation / : / positive regulation of adipose tissue development / Regulation of lipid metabolism by PPARalpha / peroxisome proliferator activated receptor signaling pathway / positive regulation of neuron differentiation / regulation of cellular response to insulin stimulus / xenobiotic metabolic process / BMAL1:CLOCK,NPAS2 activates circadian expression / SUMOylation of transcription cofactors / Activation of gene expression by SREBF (SREBP) / response to progesterone / cerebellum development / nuclear estrogen receptor binding / nuclear receptor binding / RNA polymerase II transcription regulatory region sequence-specific DNA binding / hippocampus development / SUMOylation of intracellular receptors / mRNA transcription by RNA polymerase II / Heme signaling / Transcriptional activation of mitochondrial biogenesis / PPARA activates gene expression / Cytoprotection by HMOX1 / cerebral cortex development / Nuclear Receptor transcription pathway / Transcriptional regulation of white adipocyte differentiation / RNA polymerase II transcription regulator complex / male gonad development / nuclear receptor activity / sequence-specific double-stranded DNA binding / : / response to estradiol / HATs acetylate histones / MLL4 and MLL3 complexes regulate expression of PPARG target genes in adipogenesis and hepatic steatosis / DNA-binding transcription activator activity, RNA polymerase II-specific / transcription regulator complex / Estrogen-dependent gene expression / DNA-binding transcription factor activity, RNA polymerase II-specific / cell differentiation / transcription coactivator activity / protein dimerization activity / nuclear body / positive regulation of apoptotic process / RNA polymerase II cis-regulatory region sequence-specific DNA binding / negative regulation of DNA-templated transcription / chromatin binding / positive regulation of gene expression / regulation of DNA-templated transcription / chromatin / positive regulation of DNA-templated transcription / protein-containing complex binding / negative regulation of transcription by RNA polymerase II / signal transduction / positive regulation of transcription by RNA polymerase II / protein-containing complex / zinc ion binding / nucleoplasm / nucleus / plasma membrane / cytosol
Similarity search - Function
Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : ...Nuclear receptor coactivator 1 / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator, Ncoa-type, interlocking / Nuclear receptor coactivator, Ncoa-type, interlocking domain superfamily / Nuclear receptor coactivator, DUF1518 / Nuclear receptor coactivator / DUF1518 / Nuclear receptor coactivator, receptor-binding domain / Nuclear receptor coactivator / : / Steroid receptor coactivator / Unstructured region on nuclear receptor coactivator protein / Nuclear receptor coactivators bHLH domain / PAS domain / Nuclear receptor coactivator, interlocking / helix loop helix domain / Myc-type, basic helix-loop-helix (bHLH) domain / Myc-type, basic helix-loop-helix (bHLH) domain profile. / Helix-loop-helix DNA-binding domain superfamily / : / PAS fold / PAS fold / PAS domain / PAS repeat profile. / PAS domain / PAS domain superfamily / Nuclear hormone receptor / Nuclear hormones receptors DNA-binding region signature. / Zinc finger, nuclear hormone receptor-type / Double treble clef zinc finger, C4 type / 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-N6H / PHOSPHATE ION / Nuclear receptor subfamily 1 group I member 2 / Nuclear receptor coactivator 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.85 Å
AuthorsHillig, R.C. / Puetter, V.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Design, Synthesis, and Pharmacological Characterization of a Neutral, Non-Prodrug Thrombin Inhibitor with Good Oral Pharmacokinetics.
Authors: Hillisch, A. / Gericke, K.M. / Allerheiligen, S. / Roehrig, S. / Schaefer, M. / Tersteegen, A. / Schulz, S. / Lienau, P. / Gnoth, M. / Puetter, V. / Hillig, R.C. / Heitmeier, S.
History
DepositionNov 14, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Nov 25, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: 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 / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1
B: Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,74613
Polymers78,3682
Non-polymers1,37811
Water6,485360
1
A: Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,5815
Polymers39,1841
Non-polymers3974
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,1658
Polymers39,1841
Non-polymers9817
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)85.356, 88.964, 105.658
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: GLY / Beg label comp-ID: GLY / End auth comp-ID: GLY / End label comp-ID: GLY / Refine code: _ / Auth seq-ID: 142 - 459 / Label seq-ID: 24 - 341

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Nuclear receptor subfamily 1 group I member 2,Nuclear receptor coactivator 1 / Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and ...Orphan nuclear receptor PAR1 / Orphan nuclear receptor PXR / Pregnane X receptor / Steroid and xenobiotic receptor / SXR / NCoA-1 / Class E basic helix-loop-helix protein 74 / bHLHe74 / Protein Hin-2 / RIP160 / Renal carcinoma antigen NY-REN-52 / Steroid receptor coactivator 1 / SRC-1


Mass: 39184.035 Da / Num. of mol.: 2 / Mutation: K129G
Source method: isolated from a genetically manipulated source
Details: PXR, RESIDUES 129-434, K129G IS A CLONING ARTIFACT; LINKER; SRC-1, RESIDUES 678-700,PXR, RESIDUES 129-434, K129G IS A CLONING ARTIFACT; LINKER; SRC-1, RESIDUES 678-700
Source: (gene. exp.) Homo sapiens (human) / Gene: NR1I2, PXR, NCOA1, BHLHE74, SRC1 / Production host: Escherichia coli (E. coli)
References: UniProt: O75469, UniProt: Q15788, histone acetyltransferase

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Non-polymers , 6 types, 371 molecules

#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: PO4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#6: Chemical ChemComp-N6H / [2-[(3-chlorophenyl)methylamino]-7-methoxy-1,3-benzoxazol-5-yl]-(2,2-dimethylmorpholin-4-yl)methanone


Mass: 429.897 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24ClN3O4 / Feature type: SUBJECT OF INVESTIGATION
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 360 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.56 Å3/Da / Density % sol: 51.94 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 1 MICROLITER PROTEIN AT 12.1 MG/ML (IN 20 MILLIMOLAR TRIS PH 7.8, 250 MILLIMOLAR NACL, 2.5 MILLIMOLAR EDTA, 5% (V/V) GLYCEROL, 5 MM DTT), PREINCUBATED WITH 25 MILLIMOLAR COMPOUND 17 (FROM ...Details: 1 MICROLITER PROTEIN AT 12.1 MG/ML (IN 20 MILLIMOLAR TRIS PH 7.8, 250 MILLIMOLAR NACL, 2.5 MILLIMOLAR EDTA, 5% (V/V) GLYCEROL, 5 MM DTT), PREINCUBATED WITH 25 MILLIMOLAR COMPOUND 17 (FROM 500 MILLIMOLAR STOCK IN DMSO) for 24 hours at 277 K, MIXED WITH 1 MICROLITER OF RESERVOIR (100 MILLIMOLAR IMIDAZOLE PH 8.0, 20 % (V/V) MPD). CRYO BUFFER 100 MILLIMOLAR IMIDAZOLE PH 8.0, 30 % (V/V) MPD

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 13, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.85→44.48 Å / Num. obs: 67925 / % possible obs: 97.9 % / Redundancy: 5.07 % / Biso Wilson estimate: 39.61 Å2 / CC1/2: 0.999 / Rrim(I) all: 0.059 / Rsym value: 0.053 / Net I/σ(I): 17.15
Reflection shellResolution: 1.85→1.96 Å / Redundancy: 5 % / Mean I/σ(I) obs: 1.82 / Num. unique obs: 10924 / CC1/2: 0.668 / Rrim(I) all: 0.977 / Rsym value: 0.878 / % possible all: 98.7

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Processing

Software
NameVersionClassification
REFMAC5.8.0238refinement
XDSJune 17, 2015data reduction
XSCALEJune 17, 2015data scaling
REFMAC5.5.0102phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3HVL

3hvl


Resolution: 1.85→44.48 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.956 / SU B: 5.569 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R: 0.113 / ESU R Free: 0.108 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.19932 2101 3.1 %RANDOM
Rwork0.17192 ---
obs0.17276 65823 97.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 41.918 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å2-0 Å2-0 Å2
2--0.25 Å2-0 Å2
3---0.35 Å2
Refinement stepCycle: LAST / Resolution: 1.85→44.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4847 0 89 360 5296
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0050.0135185
X-RAY DIFFRACTIONr_bond_other_d0.0010.0174914
X-RAY DIFFRACTIONr_angle_refined_deg1.3081.6517002
X-RAY DIFFRACTIONr_angle_other_deg1.2651.57411398
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1925635
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.87321.75280
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.97815969
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.1371538
X-RAY DIFFRACTIONr_chiral_restr0.0740.2652
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.025686
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021110
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_it3.0813.0552447
X-RAY DIFFRACTIONr_mcbond_other3.0813.0542446
X-RAY DIFFRACTIONr_mcangle_it4.676.8273068
X-RAY DIFFRACTIONr_mcangle_other4.6696.8293069
X-RAY DIFFRACTIONr_scbond_it4.2093.5882738
X-RAY DIFFRACTIONr_scbond_other4.2083.592739
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other6.6257.7493920
X-RAY DIFFRACTIONr_long_range_B_refined9.44338.3465987
X-RAY DIFFRACTIONr_long_range_B_other9.40437.9445911
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 9742 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.1 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.849→1.897 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.324 154 -
Rwork0.301 4821 -
obs--97.8 %
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)
10.7286-0.2822-0.51480.46510.11991.351-0.01080.0765-0.0316-0.0259-0.13910.0309-0.1509-0.07970.14990.06330.0141-0.00020.0446-0.0150.07169.15728.50830.275
215.841-4.9965-1.49777.16-1.01087.1271-0.28120.9102-0.2728-0.065-0.07860.30050.767-0.6110.35980.0913-0.0430.01480.2261-0.15460.14311.61612.01518.363
31.5920.3640.15020.6578-0.53340.66370.0795-0.0854-0.09630.0118-0.0214-0.03560.04570.025-0.05810.0586-0.0114-0.01830.0597-0.00780.054954.14942.1147.773
41.6784-1.59054.7413.5942-1.750517.12560.04240.15690.10370.2543-0.0327-0.43610.71690.5231-0.00970.3549-0.05280.13130.127-0.15070.272555.77427.884-8.246
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A142 - 434
2X-RAY DIFFRACTION2A443 - 460
3X-RAY DIFFRACTION3B138 - 431
4X-RAY DIFFRACTION4B444 - 461

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