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 

Starting Model: experimental
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This is version 1.2 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: https://doi.org/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. 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1167Homo sapiensMutation(s): 1 
Gene Names: PIN1
EC: 5.2.1.8
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
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
RZD
Query on RZD

Download Ideal Coordinates CCD File 
B [auth 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
PE8
Query on PE8

Download Ideal Coordinates CCD File 
C [auth A]3,6,9,12,15,18,21-HEPTAOXATRICOSANE-1,23-DIOL
C16 H34 O9
GLZWNFNQMJAZGY-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
RZD PDBBind:  3NTP IC50: 1.20e+4 (nM) from 1 assay(s)
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

  • 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
  • Version 1.1: 2023-12-27
    Changes: Data collection, Database references, Derived calculations
  • Version 1.2: 2024-04-03
    Changes: Refinement description