2ITK

human Pin1 bound to D-PEPTIDE


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.222 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for high-affinity peptide inhibition of human Pin1.

Zhang, Y.Daum, S.Wildemann, D.Zhou, X.Z.Verdecia, M.A.Bowman, M.E.Lucke, C.Hunter, T.Lu, K.P.Fischer, G.Noel, J.P.

(2007) Acs Chem.Biol. 2: 320-328

  • DOI: 10.1021/cb7000044
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Human Pin1 is a key regulator of cell-cycle progression and plays growth-promoting roles in human cancers. High-affinity inhibitors of Pin1 may provide a unique opportunity for disrupting oncogenic pathways. Here we report two high-resolution X-ray c ...

    Human Pin1 is a key regulator of cell-cycle progression and plays growth-promoting roles in human cancers. High-affinity inhibitors of Pin1 may provide a unique opportunity for disrupting oncogenic pathways. Here we report two high-resolution X-ray crystal structures of human Pin1 bound to non-natural peptide inhibitors. The structures of the bound high-affinity peptides identify a type-I beta-turn conformation for Pin1 prolyl peptide isomerase domain-peptide binding and an extensive molecular interface for high-affinity recognition. Moreover, these structures suggest chemical elements that may further improve the affinity and pharmacological properties of future peptide-based Pin inhibitors. Finally, an intramolecular hydrogen bond observed in both peptide complexes mimics the cyclic conformation of FK506 and rapamycin. Both FK506 and rapamycin are clinically important inhibitors of other peptidyl-prolyl cis-trans isomerases. This comparative discovery suggests that a cyclic peptide polyketide bridge, like that found in FK506 and rapamycin or a similar linkage, may significantly improve the binding affinity of structure-based Pin1 inhibitors.


    Organizational Affiliation

    The Jack H. Skirball Center for Chemical Biology and Proteomics, The Salk Institute for Biological Studies, La Jolla, California 92037, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1
A
167Homo sapiensMutation(s): 1 
Gene Names: PIN1
EC: 5.2.1.8
Find proteins for Q13526 (Homo sapiens)
Go to Gene View: PIN1
Go to UniProtKB:  Q13526
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
D-Peptide
B
7N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PE4
Query on PE4

Download SDF File 
Download CCD File 
A
2-{2-[2-(2-{2-[2-(2-ETHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHOXY]-ETHOXY}-ETHANOL
POLYETHYLENE GLYCOL PEG4000
C16 H34 O8
PJWQOENWHPEPKI-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
NH2
Query on NH2
B
NON-POLYMERH2 N

--

NAL
Query on NAL
B
L-PEPTIDE LINKINGC13 H13 N O2ALA
YCP
Query on YCP
B
L-peptide linkingC6 H11 N O2

--

D11
Query on D11
B
D-PEPTIDE LINKINGC4 H10 N O6 P

--

ACE
Query on ACE
B
NON-POLYMERC2 H4 O

--

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.222 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 68.727α = 90.00
b = 68.727β = 90.00
c = 79.957γ = 120.00
Software Package:
Software NamePurpose
AMoREphasing
HKL-2000data reduction
HKL-2000data scaling
REFMACrefinement
MOSFLMdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2006-10-19 
  • Released Date: 2007-05-22 
  • Deposition Author(s): Noel, J.P., Zhang, Y.

Revision History 

  • Version 1.0: 2007-05-22
    Type: Initial release
  • Version 1.1: 2008-05-01
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance