3I6C

Structure-Based Design of Novel PIN1 Inhibitors (II)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.164 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structure-based design of novel human Pin1 inhibitors (II).

Dong, L.Marakovits, J.Hou, X.Guo, C.Greasley, S.Dagostino, E.Ferre, R.Johnson, M.C.Kraynov, E.Thomson, J.Pathak, V.Murray, B.W.

(2010) Bioorg.Med.Chem.Lett. 20: 2210-2214

  • DOI: 10.1016/j.bmcl.2010.02.033
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Following the discovery of a novel series of phosphate-containing small molecular Pin1 inhibitors, the drug design strategy shifted to replacement of the phosphate group with an isostere with potential better pharmaceutical properties. The initial lo ...

    Following the discovery of a novel series of phosphate-containing small molecular Pin1 inhibitors, the drug design strategy shifted to replacement of the phosphate group with an isostere with potential better pharmaceutical properties. The initial loss in potency of carboxylate analogs was likely due to weaker charge-charge interactions in the putative phosphate binding pocket and was subsequently recovered by structure-based optimization of ligand-protein interactions in the proline binding site, leading to the discovery of a sub-micromolar non-phosphate small molecular Pin1 inhibitor.


    Organizational Affiliation

    Pfizer Global Research and Development, 10770 Science Center Drive, San Diego, CA 92121, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
A, B
123Homo sapiensMutation(s): 2 
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 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GIA
Query on GIA

Download SDF File 
Download CCD File 
A, B
3-fluoro-N-(naphthalen-2-ylcarbonyl)-D-phenylalanine
C20 H16 F N O3
JVSARVOIIXAOKH-GOSISDBHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GIAIC50: 12000 nM (98) BINDINGDB
GIAKi: 12000 nM (98) BINDINGDB
GIAKi: 12000 nM BINDINGMOAD
GIAKi: 12000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.3 Å
  • R-Value Free: 0.214 
  • R-Value Work: 0.164 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 117.967α = 90.00
b = 36.648β = 100.99
c = 51.293γ = 90.00
Software Package:
Software NamePurpose
DENZOdata reduction
HKL-2000data collection
SHELXL-97refinement
ARP/wARPmodel building
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-04-21
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance