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- PDB-7ekv: Crystal Structure of human Pin1 complexed with a covalent inhibitor -

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Basic information

Entry
Database: PDB / ID: 7ekv
TitleCrystal Structure of human Pin1 complexed with a covalent inhibitor
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE / covalent / inhibitor / complex
Function / homology
Function and homology information


cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of SMAD protein signal transduction ...cis-trans isomerase activity / phosphothreonine residue binding / negative regulation of cell motility / ubiquitin ligase activator activity / regulation of protein localization to nucleus / GTPase activating protein binding / postsynaptic cytosol / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division / negative regulation of SMAD protein signal transduction / PI5P Regulates TP53 Acetylation / negative regulation of amyloid-beta formation / cytoskeletal motor activity / phosphoserine residue binding / RHO GTPases Activate NADPH Oxidases / protein peptidyl-prolyl isomerization / positive regulation of protein dephosphorylation / ciliary basal body / positive regulation of GTPase activity / regulation of cytokinesis / negative regulation of protein binding / peptidylprolyl isomerase / peptidyl-prolyl cis-trans isomerase activity / Negative regulators of DDX58/IFIH1 signaling / phosphoprotein binding / synapse organization / negative regulation of transforming growth factor beta receptor signaling pathway / regulation of protein phosphorylation / regulation of protein stability / tau protein binding / neuron differentiation / negative regulation of protein catabolic process / negative regulation of ERK1 and ERK2 cascade / ISG15 antiviral mechanism / beta-catenin binding / positive regulation of canonical Wnt signaling pathway / positive regulation of protein binding / midbody / regulation of gene expression / Regulation of TP53 Activity through Phosphorylation / protein stabilization / response to hypoxia / nuclear speck / positive regulation of protein phosphorylation / cell cycle / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytoplasm / cytosol
Similarity search - Function
Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues ...Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site / PpiC-type peptidyl-prolyl cis-trans isomerase signature. / PPIC-type PPIASE domain / PpiC-type peptidyl-prolyl cis-trans isomerase family profile. / Peptidyl-prolyl cis-trans isomerase, PpiC-type / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Peptidyl-prolyl cis-trans isomerase domain superfamily
Similarity search - Domain/homology
Chem-J50 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsLiu, L. / Li, J.
CitationJournal: J.Med.Chem. / Year: 2022
Title: Computational and Structure-Based Development of High Potent Cell-Active Covalent Inhibitor Targeting the Peptidyl-Prolyl Isomerase NIMA-Interacting-1 (Pin1).
Authors: Liu, L. / Zhu, R. / Li, J. / Pei, Y. / Wang, S. / Xu, P. / Wang, M. / Wen, Y. / Zhang, H. / Du, D. / Ding, H. / Jiang, H. / Chen, K. / Zhou, B. / Yu, L. / Luo, C.
History
DepositionApr 6, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 16, 2022Provider: repository / Type: Initial release
Revision 1.1Feb 23, 2022Group: 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 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1323
Polymers20,3571
Non-polymers7752
Water3,081171
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area190 Å2
ΔGint-0 kcal/mol
Surface area8640 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.637, 68.637, 79.813
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number152
Space group name H-MP3121

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Components

#1: Protein Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 / Peptidyl-prolyl cis-trans isomerase Pin1 / PPIase Pin1 / Rotamase Pin1


Mass: 20356.572 Da / Num. of mol.: 1 / Mutation: R14A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: PIN1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13526, peptidylprolyl isomerase
#2: Chemical ChemComp-J50 / 8-(2-chloroacetyl)-4-((5-phenylfuran-2-yl)methyl)-1-thia-4,8-diazaspiro[4.5]decan-3-one


Mass: 404.910 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H21ClN2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PE8 / 3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL


Mass: 370.436 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H34O9
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 171 / 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: 2.67 Å3/Da / Density % sol: 58.15 %
Crystal growTemperature: 277.15 K / Method: vapor diffusion, hanging drop / pH: 7.4
Details: 2M Ammonium Sulfate, 1% PEG400, 100mM HEPES, pH 7.5
PH range: 7.4-7.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9785 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 29, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 16326 / % possible obs: 99.93 % / Redundancy: 19.2 % / Rmerge(I) obs: 0.08031 / Net I/σ(I): 41.92
Reflection shellResolution: 1.95→2.02 Å / Num. unique obs: 1597 / CC1/2: 0.988 / CC star: 0.997 / % possible all: 99.94

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Processing

Software
NameVersionClassification
PHENIX1.17.1_3660refinement
PDB_EXTRACT3.27data extraction
HKL-3000data reduction
HKL-3000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NTP

3ntp


Resolution: 1.95→33.13 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 22.24 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2349 1630 9.98 %
Rwork0.1974 14696 -
obs0.2011 16326 99.88 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 57.26 Å2 / Biso mean: 20.1142 Å2 / Biso min: 4.99 Å2
Refinement stepCycle: final / Resolution: 1.95→33.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1165 0 51 171 1387
Biso mean--24.06 28.29 -
Num. residues----146
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 12

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.95-2.010.29071330.23631172130599
2.01-2.070.24951340.227212151349100
2.07-2.140.25651350.209612011336100
2.14-2.230.23541380.209312161354100
2.23-2.330.2531340.217611991333100
2.33-2.450.28391340.221612321366100
2.46-2.610.26081280.210712101338100
2.61-2.810.26631390.207912101349100
2.81-3.090.23551330.198712371370100
3.09-3.540.23741420.187912261368100
3.54-4.460.20591350.155312551390100
4.46-33.130.18911450.193213231468100

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