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- PDB-7f0m: Crystal Structure of human Pin1 complexed with a potent covalent ... -

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Basic information

Entry
Database: PDB / ID: 7f0m
TitleCrystal Structure of human Pin1 complexed with a potent 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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / mitogen-activated protein kinase kinase binding / regulation of mitotic nuclear division ...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 / protein targeting to mitochondrion / protein peptidyl-prolyl isomerization / 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 / postsynaptic cytosol / RHO GTPases Activate NADPH Oxidases / phosphoserine residue binding / negative regulation of protein binding / positive regulation of GTPase activity / peptidyl-prolyl cis-trans isomerase activity / regulation of cytokinesis / RNA polymerase II CTD heptapeptide repeat P3 isomerase activity / RNA polymerase II CTD heptapeptide repeat P6 isomerase activity / peptidylprolyl isomerase / phosphoprotein binding / Negative regulators of DDX58/IFIH1 signaling / negative regulation of transforming growth factor beta receptor signaling pathway / synapse organization / negative regulation of ERK1 and ERK2 cascade / regulation of protein stability / negative regulation of protein catabolic process / beta-catenin binding / tau protein binding / ISG15 antiviral mechanism / neuron differentiation / positive regulation of canonical Wnt signaling pathway / positive regulation of protein phosphorylation / regulation of gene expression / midbody / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / response to hypoxia / protein stabilization / nuclear speck / ciliary basal body / glutamatergic synapse / positive regulation of transcription by RNA polymerase II / nucleoplasm / nucleus / cytosol / cytoplasm
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. ...: / 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-0BF / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
DepositionJun 5, 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
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Assembly

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


Theoretical massNumber of molelcules
Total (without water)84,55212
Polymers81,4264
Non-polymers3,1258
Water8,611478
1
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1383
Polymers20,3571
Non-polymers7812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-0 kcal/mol
Surface area8760 Å2
2
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1383
Polymers20,3571
Non-polymers7812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-1 kcal/mol
Surface area8770 Å2
3
C: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1383
Polymers20,3571
Non-polymers7812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area8370 Å2
4
D: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,1383
Polymers20,3571
Non-polymers7812
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-0 kcal/mol
Surface area8750 Å2
Unit cell
Length a, b, c (Å)54.259, 73.685, 87.885
Angle α, β, γ (deg.)90.000, 101.050, 90.000
Int Tables number4
Space group name H-MP1211

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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.: 4 / 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-0BF / 8-(2-chloranylethanoyl)-4-[(5-naphthalen-1-ylfuran-2-yl)methyl]-1-thia-4,8-diazaspiro[4.5]decan-3-one


Mass: 454.969 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C24H23ClN2O3S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-P33 / 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL / HEPTAETHYLENE GLYCOL / PEG330


Mass: 326.383 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C14H30O8 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 478 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.12 Å3/Da / Density % sol: 41.92 %
Crystal growTemperature: 289.15 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 30% PEG400, 100mM Tris, pH 8.0 / PH range: 7.6-8.0

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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: May 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9785 Å / Relative weight: 1
ReflectionResolution: 1.9→29.61 Å / Num. obs: 53567 / % possible obs: 99.58 % / Redundancy: 5.8 % / CC1/2: 0.999 / Rmerge(I) obs: 0.06213 / Net I/σ(I): 16.83
Reflection shellResolution: 1.9→1.968 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.2783 / Mean I/σ(I) obs: 5.5 / Num. unique obs: 5323

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Processing

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

3ntp


Resolution: 1.9→29.61 Å / SU ML: 0.22 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 30.44 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2475 1998 3.74 %
Rwork0.2152 51453 -
obs0.2164 53451 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 60.69 Å2 / Biso mean: 23.7461 Å2 / Biso min: 9.48 Å2
Refinement stepCycle: final / Resolution: 1.9→29.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4660 0 208 478 5346
Biso mean--20.44 30.57 -
Num. residues----584
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.9-1.970.25821990.223551095308100
1.97-2.050.291990.211651275326100
2.05-2.140.22321980.207151175315100
2.14-2.250.25332010.207251655366100
2.25-2.390.24561980.218251035301100
2.39-2.580.27012000.227951505350100
2.58-2.840.28691990.222451515350100
2.84-3.250.24312000.2151435343100
3.25-4.090.23762010.196951755376100
4.09-29.610.22532030.23055213541699

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