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- PDB-3ikg: Structure-Based Design of Novel PIN1 Inhibitors (I) -

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Basic information

Entry
Database: PDB / ID: 3ikg
TitleStructure-Based Design of Novel PIN1 Inhibitors (I)
ComponentsPeptidyl-prolyl cis-trans isomerase NIMA-interacting 1
KeywordsISOMERASE / SBDD / PPIase / Cell cycle / Small Molecule / Nucleus / Phosphoprotein / Rotamase / PEPTIDYL-PROLYL CIS-TRANS ISOMERASE
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 / Chitinase A; domain 3 - #40 / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / Chitinase A; domain 3 ...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 / Chitinase A; domain 3 - #40 / WW domain / WW/rsp5/WWP domain signature. / WW domain superfamily / Chitinase A; domain 3 / WW/rsp5/WWP domain profile. / Domain with 2 conserved Trp (W) residues / WW domain / Peptidyl-prolyl cis-trans isomerase domain superfamily / Roll / Alpha Beta
Similarity search - Domain/homology
Chem-J8Z / Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / DIFFERENCE FOURIER / Resolution: 1.86 Å
AuthorsParge, H. / Ferre, R.A. / Greasley, S. / Matthews, D.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2009
Title: Structure-based design of novel human Pin1 inhibitors (I).
Authors: Guo, C. / Hou, X. / Dong, L. / Dagostino, E. / Greasley, S. / Ferre, R. / Marakovits, J. / Johnson, M.C. / Matthews, D. / Mroczkowski, B. / Parge, H. / Vanarsdale, T. / Popoff, I. / Piraino, ...Authors: Guo, C. / Hou, X. / Dong, L. / Dagostino, E. / Greasley, S. / Ferre, R. / Marakovits, J. / Johnson, M.C. / Matthews, D. / Mroczkowski, B. / Parge, H. / Vanarsdale, T. / Popoff, I. / Piraino, J. / Margosiak, S. / Thomson, J. / Los, G. / Murray, B.W.
History
DepositionAug 5, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 22, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 30, 2016Group: Other
Revision 1.3Jan 24, 2018Group: Structure summary / Category: audit_author / Item: _audit_author.name
Revision 1.4Oct 13, 2021Group: Database references / Derived calculations / Category: database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5Sep 6, 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
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,1314
Polymers27,3242
Non-polymers8072
Water3,009167
1
A: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0662
Polymers13,6621
Non-polymers4031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,0662
Polymers13,6621
Non-polymers4031
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)118.255, 36.530, 51.320
Angle α, β, γ (deg.)90.00, 100.40, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-205-

HOH

21A-232-

HOH

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Components

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


Mass: 13662.197 Da / Num. of mol.: 2 / Fragment: UNP residues 45-163, PIN1 PPIASE DOMAIN / Mutation: K77Q,K82Q
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-J8Z / (2R)-2-[(1-benzothiophen-2-ylcarbonyl)amino]-3-(3-methylphenyl)propyl phosphate


Mass: 403.389 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H18NO5PS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / Source method: isolated from a natural source / Formula: H2O

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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: 1.77 Å3/Da / Density % sol: 38.35 %
Crystal growTemperature: 286 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.2M ammonium sulfate, 0.9M Na Citrate, 5mM TCEP, 100mM HEPES: Compound @ 500uM soaked into apo crystal for 60hrs. , pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 286K

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH2R / Wavelength: 1 Å
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Jun 20, 2000 / Details: OSMIC BLUE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.86→10 Å / Num. all: 18140 / Num. obs: 18140 / % possible obs: 99.1 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 2 / Redundancy: 4.39 % / Rmerge(I) obs: 0.061 / Net I/σ(I): 20.7
Reflection shellResolution: 1.86→1.93 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.404 / Mean I/σ(I) obs: 3.6 / Num. unique all: 1684 / Rsym value: 0.404 / % possible all: 91.5

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Processing

Software
NameClassification
HKL-2000data collection
SHELXmodel building
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
SHELXphasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 3IK8 Apo PPIase K7782Q

3ik8


Resolution: 1.86→10 Å / Num. parameters: 8007 / Num. restraintsaints: 7470 / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rwork0.2062 ---
all0.2062 18140 --
obs0.2062 18140 99.6 %-
Rfree---None selected
Refine analyzeNum. disordered residues: 0 / Occupancy sum hydrogen: 0 / Occupancy sum non hydrogen: 2001
Refinement stepCycle: LAST / Resolution: 1.86→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1781 0 54 167 2002
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.005
X-RAY DIFFRACTIONs_angle_d0.02
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0255
X-RAY DIFFRACTIONs_zero_chiral_vol0.029
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.035
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.019
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.076
X-RAY DIFFRACTIONs_approx_iso_adps0

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