4TOT

Crystal structure of rat cyclophilin D in complex with a potent nonimmunosuppressive inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 

wwPDB Validation   3D Report Full Report


This is version 1.0 of the entry. See complete history


Literature

Potent nonimmunosuppressive cyclophilin inhibitors with improved pharmaceutical properties and decreased transporter inhibition.

Fu, J.Tjandra, M.Becker, C.Bednarczyk, D.Capparelli, M.Elling, R.Hanna, I.Fujimoto, R.Furegati, M.Karur, S.Kasprzyk, T.Knapp, M.Leung, K.Li, X.Lu, P.Mergo, W.Miault, C.Ng, S.Parker, D.Peng, Y.Roggo, S.Rivkin, A.Simmons, R.L.Wang, M.Wiedmann, B.Weiss, A.H.Xiao, L.Xie, L.Xu, W.Yifru, A.Yang, S.Zhou, B.Sweeney, Z.K.

(2014) J Med Chem 57: 8503-8516

  • DOI: 10.1021/jm500862r
  • Primary Citation of Related Structures:  
    4TOT

  • PubMed Abstract: 
  • Nonimmunosuppressive cyclophilin inhibitors have demonstrated efficacy for the treatment of hepatitis C infection (HCV). However, alisporivir, cyclosporin A, and most other cyclosporins are potent inhibitors of OATP1B1, MRP2, MDR1, and other important drug transporters ...

    Nonimmunosuppressive cyclophilin inhibitors have demonstrated efficacy for the treatment of hepatitis C infection (HCV). However, alisporivir, cyclosporin A, and most other cyclosporins are potent inhibitors of OATP1B1, MRP2, MDR1, and other important drug transporters. Reduction of the side chain hydrophobicity of the P4 residue preserves cyclophilin binding and antiviral potency while decreasing transporter inhibition. Representative inhibitor 33 (NIM258) is a less potent transporter inhibitor relative to previously described cyclosporins, retains anti-HCV activity in cell culture, and has an acceptable pharmacokinetic profile in rats and dogs. An X-ray structure of 33 bound to rat cyclophilin D is reported.


    Organizational Affiliation

    Novartis Institutes for Biomedical Research , 4560 Horton Street, Emeryville, California 94608, United States.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Peptidyl-prolyl cis-trans isomerase F, mitochondrialA, B, C, D165Rattus norvegicusMutation(s): 1 
Gene Names: Ppif
EC: 5.2.1.8
UniProt
Find proteins for P29117 (Rattus norvegicus)
Explore P29117 
Go to UniProtKB:  P29117
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
nonimmunosuppressive inhibitorE, F, G, H11synthetic constructMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Modified Residues  5 Unique
IDChainsTypeFormula2D DiagramParent
34E
Query on 34E
E, F, G, HL-PEPTIDE LINKINGC13 H27 N3 O3VAL
ABA
Query on ABA
E, F, G, HL-PEPTIDE LINKINGC4 H9 N O2ALA
BMT
Query on BMT
E, F, G, HL-PEPTIDE LINKINGC10 H19 N O3THR
MLE
Query on MLE
E, F, G, HL-PEPTIDE LINKINGC7 H15 N O2LEU
MVA
Query on MVA
E, F, G, HL-PEPTIDE LINKINGC6 H13 N O2VAL
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 2
IDChainsNameType/Class2D Diagram3D Interactions
PRD_002115
Query on PRD_002115
E, F, G, Hnonimmunosuppressive inhibitorCyclic peptide /  Inhibitor Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.39 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.196 
  • R-Value Observed: 0.198 
  • Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.197α = 89.95
b = 57.286β = 83.81
c = 75.274γ = 89.86
Software Package:
Software NamePurpose
BUSTERrefinement

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-11-12
    Type: Initial release