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- PDB-8cce: The Fk1 domain of FKBP51 in complex with 2-(3-((R)-1-(((S)-1-((S)... -

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Basic information

Entry
Database: PDB / ID: 8cce
TitleThe Fk1 domain of FKBP51 in complex with 2-(3-((R)-1-(((S)-1-((S)-2-(5-chlorothiophen-2-yl)butanoyl)piperidine-2-carbonyl)oxy)-3-(3,4-dimethoxyphenyl)propyl)phenoxy)acetic acid
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / FKBP51 / SAFit / Inhibitor
Function / homology
Function and homology information


FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding ...FK506 binding / MECP2 regulates neuronal receptors and channels / chaperone-mediated protein folding / heat shock protein binding / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / ESR-mediated signaling / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / response to bacterium / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytosol / cytoplasm
Similarity search - Function
: / Tetratricopeptide repeat / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats ...: / Tetratricopeptide repeat / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat region circular profile. / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
Chem-UCF / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å
AuthorsMeyners, C. / Knaup, F.H. / Walz, C.M. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: J.Med.Chem. / Year: 2023
Title: Structure-Based Discovery of a New Selectivity-Enabling Motif for the FK506-Binding Protein 51.
Authors: Knaup, F.H. / Meyners, C. / Sugiarto, W.O. / Wedel, S. / Springer, M. / Walz, C. / Geiger, T.M. / Schmidt, M. / Sisignano, M. / Hausch, F.
History
DepositionJan 27, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 26, 2023Provider: repository / Type: Initial release
Revision 1.1May 10, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Feb 7, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,7403
Polymers14,0041
Non-polymers7362
Water1,74797
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area280 Å2
ΔGint-1 kcal/mol
Surface area6580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.392, 48.342, 57.276
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase FKBP5 / PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated ...PPIase FKBP5 / 51 kDa FK506-binding protein / FKBP-51 / 54 kDa progesterone receptor-associated immunophilin / Androgen-regulated protein 6 / FF1 antigen / FK506-binding protein 5 / FKBP-5 / FKBP54 / p54 / HSP90-binding immunophilin / Rotamase


Mass: 14004.026 Da / Num. of mol.: 1 / Mutation: A19T, C103A, C107I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FKBP5, AIG6, FKBP51 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-UCF / 2-[3-[(1~{R})-1-[(2~{S})-1-[(2~{S})-2-(5-chloranylthiophen-2-yl)butanoyl]piperidin-2-yl]carbonyloxy-3-(3,4-dimethoxyphenyl)propyl]phenoxy]ethanoic acid


Mass: 644.175 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H38ClNO8S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / 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: 2.29 Å3/Da / Density % sol: 46.36 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 22% PEG3350, 0.1 M HEPES pH 7.5, 0.2 M ammonium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.9184 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Dec 18, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.4→46.39 Å / Num. obs: 25513 / % possible obs: 98.3 % / Redundancy: 6.3 % / CC1/2: 1 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.031 / Rrim(I) all: 0.059 / Net I/σ(I): 16.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
7.67-46.395.40.01720010.010.02
1.4-1.426.21.46112180.7360.9481.75

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Processing

Software
NameVersionClassification
REFMAC5.8.0403refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4TW7

4tw7


Resolution: 1.4→36.97 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.337 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.066 / ESU R Free: 0.07
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2337 1276 5.01 %
Rwork0.1977 24193 -
all0.199 --
obs-25469 97.928 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 22.432 Å2
Baniso -1Baniso -2Baniso -3
1-4.652 Å20 Å2-0 Å2
2---2.895 Å20 Å2
3----1.757 Å2
Refinement stepCycle: LAST / Resolution: 1.4→36.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms923 0 50 97 1070
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.012992
X-RAY DIFFRACTIONr_bond_other_d0.0020.017955
X-RAY DIFFRACTIONr_angle_refined_deg2.0011.7051334
X-RAY DIFFRACTIONr_angle_other_deg0.7371.6422207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.0325120
X-RAY DIFFRACTIONr_dihedral_angle_2_deg4.24653
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.99910159
X-RAY DIFFRACTIONr_dihedral_angle_6_deg19.1881034
X-RAY DIFFRACTIONr_chiral_restr0.0940.2146
X-RAY DIFFRACTIONr_chiral_restr_other0.6920.211
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.021093
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02202
X-RAY DIFFRACTIONr_nbd_refined0.2090.2167
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1940.2912
X-RAY DIFFRACTIONr_nbtor_refined0.1840.2506
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0860.2538
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1890.272
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1320.25
X-RAY DIFFRACTIONr_nbd_other0.1310.226
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.3130.28
X-RAY DIFFRACTIONr_mcbond_it1.3711.209492
X-RAY DIFFRACTIONr_mcbond_other1.3711.209492
X-RAY DIFFRACTIONr_mcangle_it2.0232.15608
X-RAY DIFFRACTIONr_mcangle_other2.0212.149609
X-RAY DIFFRACTIONr_scbond_it2.0791.381500
X-RAY DIFFRACTIONr_scbond_other2.0781.383501
X-RAY DIFFRACTIONr_scangle_it3.1582.439726
X-RAY DIFFRACTIONr_scangle_other3.1562.441727
X-RAY DIFFRACTIONr_lrange_it6.08614.0611122
X-RAY DIFFRACTIONr_lrange_other6.02813.2971105
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.4-1.4360.37920.36117230.36218790.7170.76796.59390.338
1.436-1.4760.357930.33116850.33218390.7580.78596.6830.298
1.476-1.5180.301960.31316440.31217900.8460.80997.20670.279
1.518-1.5650.269800.28816290.28717510.8890.84797.60140.25
1.565-1.6160.29700.27115720.27216790.8560.85397.79630.232
1.616-1.6730.334760.2715430.27316490.8510.86498.18070.225
1.673-1.7360.237940.24814320.24815870.9060.90796.15630.21
1.736-1.8070.251660.2214180.22215170.930.93497.82470.187
1.807-1.8870.208710.18813700.18914660.9620.96798.29470.164
1.887-1.9780.197750.16513230.16714190.9720.9898.52010.148
1.978-2.0850.171500.15512690.15613330.9760.98398.94970.141
2.085-2.2110.213740.15912010.16212950.9690.98398.45560.146
2.211-2.3630.253720.17410970.17911800.9560.9899.06780.164
2.363-2.5520.246560.17410700.17811350.9690.9899.2070.163
2.552-2.7940.228550.1939720.19510360.9660.97599.13130.185
2.794-3.1220.186460.1958800.1949450.9750.97597.98940.195
3.122-3.60.245320.1938050.1958460.9680.97798.93620.199
3.6-4.3990.193310.1646960.1657300.9770.98499.5890.178
4.399-6.1770.201270.1715340.1725770.9840.98597.2270.198
6.177-36.970.321200.2163300.2213550.8880.96598.59150.25
Refinement TLS params.Method: refined / Origin x: -5.4298 Å / Origin y: -1.9631 Å / Origin z: 14.2348 Å
111213212223313233
T0.0063 Å20.0043 Å2-0.0055 Å2-0.1073 Å2-0.004 Å2--0.0884 Å2
L1.6813 °2-0.1766 °2-0.6232 °2-2.76 °2-0.2708 °2--2.0801 °2
S-0.026 Å °0.0265 Å °-0.1213 Å °-0.1187 Å °0.0045 Å °0.1102 Å °0.0362 Å °-0.0976 Å °0.0214 Å °
Refinement TLS groupSelection: ALL

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