Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 18.38 kDa 
• Atom Count: 1485 
• Residue Count: 165 
• Unique protein chains: 1

6GJR

Cyclophilin A complexed with tri-vector ligand 9.

• DOI: 10.2210/pdb6GJR/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-05-16 Released: 2018-11-07 
• Deposition Author(s): Georgiou, C., De Simone, A., Walkinshaw, M.D., Michel, J.
• Funding Organization(s): European Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.262 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 

Literature

A computationally designed binding mode flip leads to a novel class of potent tri-vector cyclophilin inhibitors.

De Simone, A., Georgiou, C., Ioannidis, H., Gupta, A.A., Juarez-Jimenez, J., Doughty-Shenton, D., Blackburn, E.A., Wear, M.A., Richards, J.P., Barlow, P.N., Carragher, N., Walkinshaw, M.D., Hulme, A.N., Michel, J.

(2019) Chem Sci 10: 542-547

• PubMed: 30746096 
• DOI: 10.1039/c8sc03831g
• Structures With Same Primary Citation


• PubMed Abstract: 
  

Cyclophilins (Cyps) are a major family of drug targets that are challenging to prosecute with small molecules because the shallow nature and high degree of conservation of the active site across human isoforms offers limited opportunities for potent and selective inhibition. Herein a computational approach based on molecular dynamics simulations and free energy calculations was combined with biophysical assays and X-ray crystallography to explore a flip in the binding mode of a reported urea-based Cyp inhibitor. This approach enabled access to a distal pocket that is poorly conserved among key Cyp isoforms, and led to the discovery of a new family of sub-micromolar cell-active inhibitors that offer unprecedented opportunities for the development of next-generation drug therapies based on Cyp inhibition. The computational approach is applicable to a broad range of organic functional groups and could prove widely enabling in molecular design.

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Organizational Affiliation: 

University of Edinburgh , Joseph Black Building, King's Buildings, David Brewster Road , Edinburgh , Scotland EH9 3FJ , UK . Email: [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Peptidyl-prolyl cis-trans isomerase A	A	165	Homo sapiens	Mutation(s): 0  Gene Names: PPIA, CYPA EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens) Go to UniProtKB:  P62937
NIH Common Fund Data Resources
PHAROS  P62937 GTEx  ENSG00000196262

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
F0W	A	ethyl 2-[[(4-aminophenyl)methyl-[(2-methyl-1,2,3,4-tetrazol-5-yl)methyl]carbamoyl]amino]ethanoate C15 H21 N7 O3 NVGCFZKHSYMFIM-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.69 Å
• R-Value Free: 0.262 
• R-Value Work: 0.200 
• R-Value Observed: 0.203 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.51	α = 90
b = 53.17	β = 90
c = 87.68	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2018-05-16 
• Released Date: 2018-11-07 
Deposition Author(s): Georgiou, C., De Simone, A., Walkinshaw, M.D., Michel, J.

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Funding Organization	Location	Grant Number
European Research Council	United Kingdom	No. 336289

Revision History 

• Version 1.0: 2018-11-07
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Data collection, Database references