3NTP

Human Pin1 complexed with reduced amide inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 

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
  • Primary Citation of Related Structures:  
    3NTP

  • 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 = fluorenylmethoxycarbonyl (Fmoc)] and 2 (R = Ac), of Pin1 were synthesized and bioassayed ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 A167Homo sapiensMutation(s): 1 
Gene Names: PIN1
EC: 5.2.1.8
Find proteins for Q13526 (Homo sapiens)
Explore Q13526 
Go to UniProtKB:  Q13526
NIH Common Fund Data Resources
PHAROS:  Q13526
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RZD
Query on RZD

Download Ideal Coordinates 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
PE8
Query on PE8

Download Ideal Coordinates CCD File 
A
3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RZDIC50 :  12000   nM  PDBBind
RZDIC50:  12000   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.76 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.231 
  • R-Value Observed: 0.233 
  • Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.847α = 90
b = 68.847β = 90
c = 79.782γ = 120
Software Package:
Software NamePurpose
HKL-2000data collection
AMoREphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

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

Revision History  (Full details and data files)

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