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

Experimental Data Snapshot

  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 

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Ligand Structure Quality Assessment 

This is version 1.3 of the entry. See complete history


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: https://doi.org/10.1016/j.bmcl.2009.11.090
  • Primary Citation of Related Structures:  
    3KAB, 3KAC, 3KAD, 3KAF, 3KAG, 3KAH, 3KAI, 3KCE

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
A, B
123Homo sapiensMutation(s): 2 
Gene Names: PIN1
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
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on 4BX

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
3-(1H-benzimidazol-2-yl)propanoic acid
C10 H10 N2 O2
Binding Affinity Annotations 
IDSourceBinding Affinity
4BX PDBBind:  3KAC IC50: 7.40e+5 (nM) from 1 assay(s)
BindingDB:  3KAC IC50: min: 1.00e+4, max: 7.40e+5 (nM) from 2 assay(s)
Experimental Data & Validation

Experimental Data

  • Resolution: 2.00 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.172 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 118.064α = 90
b = 36.576β = 101.11
c = 51.328γ = 90
Software Package:
Software NamePurpose
CrystalCleardata collection
d*TREKdata reduction
d*TREKdata scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment 

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.3: 2023-11-01
    Changes: Data collection, Refinement description