3NTP

Human Pin1 complexed with reduced amide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.762 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.231 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

A reduced-amide inhibitor of Pin1 binds in a conformation resembling a twisted-amide transition state.

Xu, G.G.Zhang, Y.Mercedes-Camacho, A.Y.Etzkorn, F.A.

(2011) Biochemistry 50: 9545-9550

  • DOI: 10.1021/bi201055c

  • PubMed Abstract: 
  • The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R-pSer-Ψ[CH(2)N]-Pro-2-(indol-3-yl)ethylamine, 1 [R ...

    The mechanism of the cell cycle regulatory peptidyl prolyl isomerase (PPIase), Pin1, was investigated using reduced-amide inhibitors designed to mimic the twisted-amide transition state. Inhibitors, R-pSer-Ψ[CH(2)N]-Pro-2-(indol-3-yl)ethylamine, 1 [R = fluorenylmethoxycarbonyl (Fmoc)] and 2 (R = Ac), of Pin1 were synthesized and bioassayed. Inhibitor 1 had an IC(50) value of 6.3 μM, which is 4.5-fold better for Pin1 than our comparable ground-state analogue, a cis-amide alkene isostere-containing inhibitor. The change of Fmoc to Ac in 2 improved aqueous solubility for structural determination and resulted in an IC(50) value of 12 μM. The X-ray structure of the complex of 2 bound to Pin1 was determined to 1.76 Å resolution. The structure revealed that the reduced amide adopted a conformation similar to the proposed twisted-amide transition state of Pin1, with a trans-pyrrolidine conformation of the prolyl ring. A similar conformation of substrate would be destabilized relative to the planar amide conformation. Three additional reduced amides, with Thr replacing Ser and l- or d-pipecolate (Pip) replacing Pro, were slightly weaker inhibitors of Pin1.


    Organizational Affiliation

    Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
A
167Homo sapiensGene 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
PE8
Query on PE8

Download SDF File 
Download CCD File 
A
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
 Ligand Interaction
RZD
Query on RZD

Download SDF File 
Download CCD File 
A
(2R)-2-(acetylamino)-3-[(2S)-2-{[2-(1H-indol-3-yl)ethyl]carbamoyl}pyrrolidin-1-yl]propyl dihydrogen phosphate
C20 H29 N4 O6 P
FDBFLFSQEGXOJR-APWZRJJASA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RZDIC50: 12000 nM BINDINGMOAD
RZDIC50: 12000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.762 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.231 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 68.847α = 90.00
b = 68.847β = 90.00
c = 79.782γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data collection
PHENIXrefinement
HKL-2000data scaling
HKL-2000data reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2010-07-05 
  • Released Date: 2012-01-04 
  • Deposition Author(s): Zhang, Y.

Revision History 

  • Version 1.0: 2012-01-04
    Type: Initial release