3KAG

Structure-guided design of alpha-amino acid-derived Pin1 inhibitors


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.202 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-guided design of alpha-amino acid-derived Pin1 inhibitors

Potter, A.J.Ray, S.Gueritz, L.Nunns, C.L.Bryant, C.J.Scrace, S.F.Matassova, N.Baker, L.M.Dokurno, P.Robinson, D.A.Surgenor, A.E.Davis, B.Murray, J.B.Richardson, C.M.Moore, J.D.

(2010) Bioorg.Med.Chem.Lett. 20: 586-590

  • DOI: 10.1016/j.bmcl.2009.11.090
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • The peptidyl prolyl cis/trans isomerase Pin1 is a promising molecular target for anti-cancer therapeutics. Here we report the structure-guided evolution of an indole 2-carboxylic acid fragment hit into a series of alpha-benzimidazolyl-substituted ami ...

    The peptidyl prolyl cis/trans isomerase Pin1 is a promising molecular target for anti-cancer therapeutics. Here we report the structure-guided evolution of an indole 2-carboxylic acid fragment hit into a series of alpha-benzimidazolyl-substituted amino acids. Examples inhibited Pin1 activity with IC(50) <100nM, but were inactive on cells. Replacement of the benzimidazole ring with a naphthyl group resulted in a 10-50-fold loss in ligand potency, but these examples downregulated biomarkers of Pin1 activity and blocked proliferation of PC3 cells.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
A
167Homo sapiensMutation(s): 1 
Gene Names: PIN1
EC: 5.2.1.8
Find proteins for Q13526 (Homo sapiens)
Go to Gene View: PIN1
Go to UniProtKB:  Q13526
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
4D7
Query on 4D7

Download SDF File 
Download CCD File 
A
3-(1H-benzimidazol-2-yl)-N-[(2-methylfuran-3-yl)carbonyl]-D-alanine
(R)-3-(1H-Benzoimidazol-2-yl)-2-[(2-methyl-furan-3-carbonyl)-amino]-propionic acid
C16 H15 N3 O4
IBXZTXVMQARJHH-CYBMUJFWSA-N
 Ligand Interaction
12P
Query on 12P

Download SDF File 
Download CCD File 
A
DODECAETHYLENE GLYCOL
POLYETHYLENE GLYCOL PEG400
C24 H50 O13
WRZXKWFJEFFURH-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
4D7IC50: 6600 nM (99) BINDINGDB
4D7IC50: 6600 nM BINDINGMOAD
4D7IC50: 6600 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.202 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 68.504α = 90.00
b = 68.504β = 90.00
c = 79.560γ = 120.00
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata scaling
REFMACrefinement
AMoREphasing
d*TREKdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance