5LUD

Structure of Cyclophilin A in complex with 2,3-Diaminopyridine

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history. 

Literature

Thermo-kinetic analysis space expansion for cyclophilin-ligand interactions - identification of a new nonpeptide inhibitor using BiacoreTM T200.

Wear, M.A., Nowicki, M.W., Blackburn, E.A., McNae, I.W., Walkinshaw, M.D.

(2017) FEBS Open Bio 7: 533-549

  • DOI: 10.1002/2211-5463.12201

  • PubMed Abstract: 

    • We have established a refined methodology for generating surface plasmon resonance sensor surfaces of recombinant his-tagged human cyclophilin-A. Our orientation-specific stabilisation approach captures his-tagged protein under 'physiological conditi ...

    We have established a refined methodology for generating surface plasmon resonance sensor surfaces of recombinant his-tagged human cyclophilin-A. Our orientation-specific stabilisation approach captures his-tagged protein under 'physiological conditions' (150 mm NaCl, pH 7.5) and covalently stabilises it on Ni2+-nitrilotriacetic acid surfaces, very briefly activated for primary amine-coupling reactions, producing very stable and active surfaces (≥ 95% specific activity) of cyclophilin-A. Variation in protein concentration with the same contact time allows straightforward generation of variable density surfaces, with essentially no loss of activity, making the protocol easily adaptable for studying numerous interactions; from very small fragments, ~ 100 Da, to large protein ligands. This new method results in an increased stability and activity of the immobilised protein and allowed us to expand the thermo-kinetic analysis space, and to determine accurate and robust thermodynamic parameters for the cyclophilin-A-cyclosporin-A interaction. Furthermore, the increased sensitivity of the surface allowed identification of a new nonpeptide inhibitor of cyclophilin-A, from a screen of a fragment library. This fragment, 2,3-diaminopyridine, bound specifically with a mean affinity of 248 ± 60 μm. The X-ray structure of this 109-Da fragment bound in the active site of cyclophilin-A was solved to a resolution of 1.25 Å (PDB: 5LUD), providing new insight into the molecular details for a potential new series of nonpeptide cyclophilin-A inhibitors.

    Organizational Affiliation: 

    The Edinburgh Protein Production Facility (EPPF) Wellcome Trust Centre for Cell Biology (WTCCB) University of Edinburgh UK.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidyl-prolyl cis-trans isomerase
A
165Homo sapiensMutation(s): 0 
Gene 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
76X
Query on 76X
Download SDF File 
Download CCD File 
A
pyridine-2,3-diamine
C5 H7 N3
ZZYXNRREDYWPLN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.25 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.193 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 42.535α = 90.00
b = 54.477β = 90.00
c = 86.808γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
REFMACrefinement
Aimlessdata scaling
REFMACphasing

Structure Validation

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View more in-depth experimental data

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Wellcome TrustUnited Kingdom081287/Z/06/Z
Wellcome TrustUnited Kingdom101527/Z/13/Z

Revision History 

  • Version 1.0: 2017-04-05
    Type: Initial release
  • Version 1.1: 2017-04-19
    Type: Database references