9GHY | pdb_00009ghy

Cyclophilin A in complex with Sanglifehrin A analogue (2R,3S,7S,10S,E)-10-(3-aminopropyl)-2,7-dimethylspiro[3,8,11-triaza-1(2,7)-quinolina-5(3,1)-pyridazinacyclopentadecaphanene-13,5'-[1,3]dioxan]-14-ene-4,6,9,12-tetraone


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free: 
    0.149 (Depositor), 0.152 (DCC) 
  • R-Value Work: 
    0.131 (Depositor), 0.140 (DCC) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 9GHY

Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Toward Dual Targeting of Catalytic and Gatekeeper Pockets in Cyclophilins Using a Macrocyclic Scaffold.

Dreizler, J.K.Meyners, C.Hausch, F.

(2024) ACS Med Chem Lett 15: 2012-2018

  • DOI: https://doi.org/10.1021/acsmedchemlett.4c00427
  • Primary Citation Related Structures: 
    9GHY

  • PubMed Abstract: 

    Cyclophilins, especially cyclophilin A, are involved in a variety of diseases, including the life cycle of many viruses. An advanced macrocyclic inhibitor of cyclophilin was reported to bind the catalytic pocket but not the neighboring gatekeeper pocket. Here we describe macrocyclic cyclophilin inhibitors bearing side chains designed to reach out to the gatekeeper pocket. After establishing a suitable synthesis allowing for late-stage modification of the relevant positions, we explored this exit vector. This culminated in a rigid ornithine-resembling analogue as a versatile building block, which was also incorporated into the macrocyclic scaffold. The use of amines as the gatekeeper-engaging modality was invalidated, but the exit vector was successfully established as a promising position for future modifications. Further work is needed to identify suitable motifs to simultaneously engage the catalytic and gatekeeper pockets in this highly developed macrocyclic scaffold.


  • Organizational Affiliation
    • Department of Chemistry and Biochemistry Clemens-Schöpf-Institute, Technical University Darmstadt, Peter-Grünberg Straße 4, 64287 Darmstadt, Germany.

Macromolecule Content 

  • Total Structure Weight: 18.87 kDa 
  • Atom Count: 1,586 
  • Modeled Residue Count: 167 
  • Deposited Residue Count: 167 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase A167Homo sapiensMutation(s): 0 
Gene Names: PPIACYPA
EC: 5.2.1.8
UniProt & NIH Common Fund Data Resources
Find proteins for P62937 (Homo sapiens)
Explore P62937 
Go to UniProtKB:  P62937
PHAROS:  P62937
GTEx:  ENSG00000196262 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62937
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A1ILH
(Subject of Investigation/LOI)

Query on A1ILH



Download:Ideal Coordinates CCD File
B [auth A](2R,3S,7S,10S,E)-10-(3-aminopropyl)-2,7-dimethylspiro[3,8,11-triaza-1(2,7)-quinolina-5(3,1)-pyridazinacyclopentadecaphanene-13,5'-[1,3]dioxan]-14-ene-4,6,9,12-tetraone
C31 H41 N7 O6
PVLNMJCQMSIFFD-WHYDHWCJSA-N
CL

Query on CL



Download:Ideal Coordinates CCD File
C [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.15 Å
  • R-Value Free:  0.149 (Depositor), 0.152 (DCC) 
  • R-Value Work:  0.131 (Depositor), 0.140 (DCC) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.854α = 90
b = 52.595β = 90
c = 89.257γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
autoXDSdata reduction
Aimlessdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
German Federal Ministry for Education and ResearchGermany03ZU1109EB
Hessian Ministry of Science, Higher Education and Art (HMWK)Germany--

Revision History  (Full details and data files)

  • Version 1.0: 2024-11-06
    Type: Initial release
  • Version 1.1: 2024-12-04
    Changes: Database references