3ODK

Discovery of cell-active phenyl-imidazole Pin1 inhibitors by structure-guided fragment evolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.251 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Discovery of cell-active phenyl-imidazole Pin1 inhibitors by structure-guided fragment evolution.

Potter, A.Oldfield, V.Nunns, C.Fromont, C.Ray, S.Northfield, C.J.Bryant, C.J.Scrace, S.F.Robinson, D.Matossova, N.Baker, L.Dokurno, P.Surgenor, A.E.Davis, B.Richardson, C.M.Murray, J.B.Moore, J.D.

(2010) Bioorg Med Chem Lett 20: 6483-6488

  • DOI: https://doi.org/10.1016/j.bmcl.2010.09.063
  • Primary Citation of Related Structures:  
    2XP3, 2XP4, 2XP5, 2XP6, 2XP7, 2XP8, 2XP9, 2XPA, 2XPB, 3ODK

  • PubMed Abstract: 

    Pin1 is an emerging oncology target strongly implicated in Ras and ErbB2-mediated tumourigenesis. Pin1 isomerizes bonds linking phospho-serine/threonine moieties to proline enabling it to play a key role in proline-directed kinase signalling. Here we report a novel series of Pin1 inhibitors based on a phenyl imidazole acid core that contains sub-μM inhibitors. Compounds have been identified that block prostate cancer cell growth under conditions where Pin1 is essential.


  • Organizational Affiliation

    Vernalis (R&D) Ltd, Granta Park, Great Abington, Cambridge CB21 6GB, United Kingdom.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1167Homo sapiensMutation(s): 1 
Gene Names: PIN1
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for Q13526 (Homo sapiens)
Explore Q13526 
Go to UniProtKB:  Q13526
PHAROS:  Q13526
GTEx:  ENSG00000127445 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ13526
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

Download Ideal Coordinates CCD File 
B [auth A]2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
ODK
Query on ODK

Download Ideal Coordinates CCD File 
C [auth A]3-pyridin-2-yl-1H-pyrazole-5-carboxylic acid
C9 H7 N3 O2
SJBWHTBPIJXUFP-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
ODK PDBBind:  3ODK IC50: 7.20e+5 (nM) from 1 assay(s)
Binding MOAD:  3ODK IC50: 7.20e+5 (nM) from 1 assay(s)
BindingDB:  3ODK IC50: 7.20e+5 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.335 
  • R-Value Work: 0.247 
  • R-Value Observed: 0.251 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.048α = 90
b = 68.048β = 90
c = 79.567γ = 120
Software Package:
Software NamePurpose
CrystalCleardata collection
AMoREphasing
REFMACrefinement
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2024-02-21
    Changes: Data collection, Database references, Derived calculations