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- PDB-9eu6: The FK1 domain of FKBP51 in complex with SAFit-analog 23j -

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Basic information

Entry
Database: PDB / ID: 9eu6
TitleThe FK1 domain of FKBP51 in complex with SAFit-analog 23j
ComponentsPeptidyl-prolyl cis-trans isomerase FKBP5
KeywordsISOMERASE / FKBP51 / Inhibitor / Complex
Function / homology
Function and homology information


Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / MECP2 regulates neuronal receptors and channels / : / heat shock protein binding / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cocaine / response to bacterium ...Modulation of host responses by IFN-stimulated genes / response to alcohol / FK506 binding / MECP2 regulates neuronal receptors and channels / : / heat shock protein binding / ESR-mediated signaling / HSP90 chaperone cycle for steroid hormone receptors (SHR) in the presence of ligand / response to cocaine / response to bacterium / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / protein folding / protein-macromolecule adaptor activity / extracellular exosome / nucleoplasm / membrane / cytoplasm / cytosol
Similarity search - Function
: / Tetratricopeptide repeat / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat profile. / Tetratricopeptide repeats ...: / Tetratricopeptide repeat / Tetratricopeptide repeat / FKBP-type peptidyl-prolyl cis-trans isomerase / FKBP-type peptidyl-prolyl cis-trans isomerase domain / FKBP-type peptidyl-prolyl cis-trans isomerase domain profile. / TPR repeat region circular profile. / Peptidyl-prolyl cis-trans isomerase domain superfamily / TPR repeat profile. / Tetratricopeptide repeats / Tetratricopeptide repeat / Tetratricopeptide-like helical domain superfamily
Similarity search - Domain/homology
: / Peptidyl-prolyl cis-trans isomerase FKBP5
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsMeyners, C. / Buffa, V. / Hausch, F.
Funding support Germany, 1items
OrganizationGrant numberCountry
German Federal Ministry for Education and Research Germany
CitationJournal: Chemmedchem / Year: 2024
Title: 1,4-Pyrazolyl-Containing SAFit-Analogues are Selective FKBP51 Inhibitors With Improved Ligand Efficiency and Drug-Like Profile.
Authors: Buffa, V. / Meyners, C. / Sugiarto, W.O. / Bauder, M. / Gaali, S. / Hausch, F.
History
DepositionMar 27, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 12, 2024Provider: repository / Type: Initial release
Revision 1.1Sep 11, 2024Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.title / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)28,5363
Polymers28,0082
Non-polymers5281
Water2,000111
1
A: Peptidyl-prolyl cis-trans isomerase FKBP5
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,5322
Polymers14,0041
Non-polymers5281
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Peptidyl-prolyl cis-trans isomerase FKBP5


Theoretical massNumber of molelcules
Total (without water)14,0041
Polymers14,0041
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)48.176, 48.176, 94.031
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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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.: 2 / 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-Gold(DE3)pLysS AG' (bacteria)
References: UniProt: Q13451, peptidylprolyl isomerase
#2: Chemical ChemComp-A1H7U / (1,5-dimethylpyrazol-4-yl)methyl (2~{S})-1-[(2~{S})-2-cyclohexyl-2-(3,4,5-trimethoxyphenyl)ethanoyl]piperidine-2-carboxylate


Mass: 527.652 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C29H41N3O6 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 45% Pentaerythritol propoxylate 5/4 PO/OH, 15% ethanol

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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 S 6M / Detector: PIXEL / Date: Sep 10, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9184 Å / Relative weight: 1
ReflectionResolution: 1.54→47.02 Å / Num. obs: 36113 / % possible obs: 99.9 % / Redundancy: 5.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.035 / Rrim(I) all: 0.06 / Net I/σ(I): 14.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all
8.44-47.025.90.0222260.9990.0150.026
1.54-1.574.51.34217780.2391.0471.711

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→41.756 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.954 / SU B: 4.096 / SU ML: 0.07 / Cross valid method: THROUGHOUT / ESU R: 0.084 / ESU R Free: 0.084
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2224 1794 4.973 %
Rwork0.1931 34281 -
all0.195 --
obs-36075 99.853 %
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: 24.975 Å2
Baniso -1Baniso -2Baniso -3
1-0.113 Å20.057 Å20 Å2
2--0.113 Å2-0 Å2
3----0.368 Å2
Refinement stepCycle: LAST / Resolution: 1.54→41.756 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1834 0 38 111 1983
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0121933
X-RAY DIFFRACTIONr_bond_other_d0.0030.0161804
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.8412622
X-RAY DIFFRACTIONr_angle_other_deg0.941.7884158
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3995252
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.19255
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.76410297
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.4811068
X-RAY DIFFRACTIONr_chiral_restr0.0810.2290
X-RAY DIFFRACTIONr_chiral_restr_other1.3390.215
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022234
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02401
X-RAY DIFFRACTIONr_nbd_refined0.1960.2325
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1890.21668
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2974
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.21004
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1250.278
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.0850.29
X-RAY DIFFRACTIONr_nbd_other0.1620.242
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.120.28
X-RAY DIFFRACTIONr_mcbond_it1.6681.961011
X-RAY DIFFRACTIONr_mcbond_other1.6661.9591011
X-RAY DIFFRACTIONr_mcangle_it2.4173.5141262
X-RAY DIFFRACTIONr_mcangle_other2.4173.5171263
X-RAY DIFFRACTIONr_scbond_it2.3072.121922
X-RAY DIFFRACTIONr_scbond_other2.3062.124923
X-RAY DIFFRACTIONr_scangle_it3.3023.8061360
X-RAY DIFFRACTIONr_scangle_other3.3013.8091361
X-RAY DIFFRACTIONr_lrange_it4.80321.012078
X-RAY DIFFRACTIONr_lrange_other4.77320.9832072
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
1.54-1.580.3261360.30625040.30726680.9270.93398.95050.305
1.58-1.6240.2861180.27925070.27926280.9360.94699.88580.28
1.624-1.6710.3341260.25824100.26225360.9260.9531000.255
1.671-1.7220.3141500.24623180.2524710.9350.9699.87860.24
1.722-1.7780.2471000.21522680.21623700.9590.96999.91560.202
1.778-1.8410.2521240.19621770.19923050.9620.97599.82650.178
1.841-1.910.2321380.17820850.18222230.9660.9791000.159
1.91-1.9880.2091000.18320270.18421280.970.97899.9530.164
1.988-2.0760.2471140.18919270.19220410.9630.9781000.174
2.076-2.1770.191860.17818600.17919480.9760.9899.89730.164
2.177-2.2940.1811220.17617750.17618970.9780.981000.165
2.294-2.4330.223720.18116780.18317510.9630.97999.94290.172
2.433-2.60.229640.17915750.18116390.9730.981000.174
2.6-2.8080.204780.19314620.19415460.9740.97799.61190.192
2.808-3.0740.278560.20213740.20414310.9580.97499.93010.206
3.074-3.4350.219500.20312520.20313020.9730.9761000.212
3.435-3.9620.205440.18510870.18511330.9740.9899.82350.198
3.962-4.8410.177520.1599010.169530.9820.9851000.178
4.841-6.8010.217480.1976930.1987410.9690.9791000.223
6.801-41.7560.29160.2114010.2144170.950.9631000.243
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)
12.21060.4580.35051.83-0.16771.8871-0.00270.0002-0.0120.04350.0377-0.16580.070.0542-0.03510.01540.01080.01510.00760.00890.05958.18456.51988.6188
23.02060.04430.79181.69150.30711.64240.0099-0.0187-0.11830.0064-0.00660.03880.0515-0.0257-0.00330.018-0.0026-0.0050.00420.01070.03474.677631.85214.9647
Refinement TLS groupSelection: ALL

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