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: 18.46 kDa 
• Atom Count: 1509 
• Modelled Residue Count: 164 
• Deposited Residue Count: 164 
• Unique protein chains: 1

5T9W

Discovery of a Potent Cyclophilin Inhibitor (Compound 5) based on Structural Simplification of Sanglifehrin A

• DOI: 10.2210/pdb5T9W/pdb

• Classification: isomerase/isomerase inhibitor
• Organism(s): Homo sapiens
• Expression System: Bacteria
• Mutation(s): No 


• Deposited: 2016-09-09 Released: 2017-01-25 
• Deposition Author(s): Appleby, T.C., Steadman, V., Pettit, P., Schmitz, U., Mackman, R.L., Schultz, B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.184 
• R-Value Work: 0.151 
• R-Value Observed: 0.154 

Literature

Discovery of Potent Cyclophilin Inhibitors Based on the Structural Simplification of Sanglifehrin A.

Steadman, V.A., Pettit, S.B., Poullennec, K.G., Lazarides, L., Keats, A.J., Dean, D.K., Stanway, S.J., Austin, C.A., Sanvoisin, J.A., Watt, G.M., Fliri, H.G., Liclican, A.C., Jin, D., Wong, M.H., Leavitt, S.A., Lee, Y.J., Tian, Y., Frey, C.R., Appleby, T.C., Schmitz, U., Jansa, P., Mackman, R.L., Schultz, B.E.

(2017) J Med Chem 60: 1000-1017

• PubMed: 28075591 
• DOI: 10.1021/acs.jmedchem.6b01329
• Primary Citation of Related Structures:  
  5T9U, 5T9W, 5T9Z, 5TA2, 5TA4


• PubMed Abstract: 
  

Cyclophilin inhibition has been a target for the treatment of hepatitis C and other diseases, but the generation of potent, drug-like molecules through chemical synthesis has been challenging. In this study, a set of macrocyclic cyclophilin inhibitors was synthesized based on the core structure of the natural product sanglifehrin A. Initial compound optimization identified the valine-m-tyrosine-piperazic acid tripeptide (Val-m-Tyr-Pip) in the sanglifehrin core, stereocenters at C14 and C15, and the hydroxyl group of the m-tyrosine (m-Tyr) residue as key contributors to compound potency. Replacing the C18-C21 diene unit of sanglifehrin with a styryl group led to potent compounds that displayed a novel binding mode in which the styrene moiety engaged in a π-stacking interaction with Arg55 of cyclophilin A (Cyp A), and the m-Tyr residue was displaced into solvent. This observation allowed further simplifications of the scaffold to generate new lead compounds in the search for orally bioavailable cyclophilin inhibitors.

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Organizational Affiliation: 

Gilead Sciences , 333 Lakeside Drive, Foster City, California 94404, United States.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Peptidyl-prolyl cis-trans isomerase A	A	164	Homo sapiens	Mutation(s): 0  Gene Names: PPIA, CYPA EC: 5.2.1.8
Find proteins for P62937 (Homo sapiens) Explore P62937  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
78E	A	3-[(3-hydroxyphenyl)methyl]-6-(propan-2-yl)-19-oxa-1,4,7,25-tetraazabicyclo[19.3.1]pentacosa-13,15-diene-2,5,8,20-tetrone C30 H42 N4 O6 ZXIFDXMZMTULOX-WDJUPVIMSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
78E	Kd:  2600   nM  Binding MOAD

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002241 (78E)	A	3-[(3-hydroxyphenyl)methyl]-6-(propan-2-yl)-19-oxa-1,4,7,25-tetraazabicyclo[19.3.1]pentacosa-13,15-diene-2,5,8,20-tetrone	Peptide-like /  Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.184 
• R-Value Work: 0.151 
• R-Value Observed: 0.154 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 64.864	α = 90
b = 84.514	β = 90
c = 68.533	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2016-09-09 
• Released Date: 2017-01-25 
Deposition Author(s): Appleby, T.C., Steadman, V., Pettit, P., Schmitz, U., Mackman, R.L., Schultz, B.

Revision History  

• Version 1.0: 2017-01-25
  Type: Initial release
  
• Version 1.1: 2017-02-08
  Changes: Database references
• Version 1.2: 2017-02-15
  Changes: Database references
• Version 1.3: 2017-03-29
  Changes: Structure summary