1W8L

Enzymatic and structural characterization of non peptide ligand cyclophilin complexes


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.179 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Enzymatic and Structural Characterization of Non-Peptide Ligand-Cyclophilin Complexes

Kontopidis, G.Taylor, P.Walkinshaw, M.

(2004) Acta Crystallogr.,Sect.D 60: 479

  • DOI: 10.1107/S0907444904000174
  • Primary Citation of Related Structures:  1W8M, 1W8V

  • PubMed Abstract: 
  • Piperidine ligands are described that provide the first examples of non-peptidic ligand structures for the cyclophilin family of proteins. Crystal structures of two ligand complexes are compared with the unliganded protein and show ligand-induced cha ...

    Piperidine ligands are described that provide the first examples of non-peptidic ligand structures for the cyclophilin family of proteins. Crystal structures of two ligand complexes are compared with the unliganded protein and show ligand-induced changes in side-chain conformation and water binding. A peptidylprolyl cis-trans-isomerase assay showed the dissociation constants of the two ligands to be 320 and 25 mM. This study also provides the first published data for both enzymatic activity and three-dimensional structure for any protein-ligand complex that binds with a high-millimolar dissociation constant. The structures may be of relevance in the field of drug design, as they suggest starting points for the design of larger tighter-binding analogues.


    Organizational Affiliation

    Structural Biochemistry Group, Department of Biochemistry, The University of Edinburgh, Michael Swann Building, King's Buildings, Edinburgh EH9 3JR, Scotland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PEPTIDYL-PROLYL CIS-TRANS ISOMERASE A
A
165Homo sapiensGene Names: PPIA (CYPA)
EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens)
Go to Gene View: PPIA
Go to UniProtKB:  P62937
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
1P3
Query on 1P3

Download SDF File 
Download CCD File 
A
(3R)-1-ACETYL-3-METHYLPIPERIDINE
C8 H15 N O
XKFPNHDGLSYZRC-SSDOTTSWSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1P3Ki: 320000000 nM BINDINGMOAD
1P3Ki: 320000000 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.179 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 36.090α = 90.00
b = 54.310β = 90.00
c = 70.970γ = 90.00
Software Package:
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
X-PLORphasing
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-09-30
    Type: Initial release
  • Version 1.1: 2011-05-08
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance