3TIK | pdb_00003tik

Sterol 14-alpha demethylase (CYP51) from Trypanosoma brucei in complex with the tipifarnib derivative 6-((4-chlorophenyl)(methoxy)(1-methyl-1H-imidazol-5-yl)methyl)-4-(2,6-difluorophenyl)-1-methylquinolin-2(1H)-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free: 
    0.243 (Depositor), 0.241 (DCC) 
  • R-Value Work: 
    0.186 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 
    0.189 (Depositor) 

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 3TIK

Ligand Structure Quality Assessment 


This is version 1.3 of the entry. See complete history

Literature

Pharmacological characterization, structural studies, and in vivo activities of anti-chagas disease lead compounds derived from tipifarnib.

Buckner, F.S.Bahia, M.T.Suryadevara, P.K.White, K.L.Shackleford, D.M.Chennamaneni, N.K.Hulverson, M.A.Laydbak, J.U.Chatelain, E.Scandale, I.Verlinde, C.L.Charman, S.A.Lepesheva, G.I.Gelb, M.H.

(2012) Antimicrob Agents Chemother 56: 4914-4921

  • DOI: https://doi.org/10.1128/AAC.06244-11
  • Primary Citation Related Structures: 
    3TIK

  • PubMed Abstract: 

    Chagas disease, caused by the protozoan pathogen Trypanosoma cruzi, remains a challenging infection due to the unavailability of safe and efficacious drugs. Inhibitors of the trypanosome sterol 14α-demethylase enzyme (CYP51), including azole antifungal drugs, are promising candidates for development as anti-Chagas disease drugs. Posaconazole is under clinical investigation for Chagas disease, although the high cost of this drug may limit its widespread use. We have previously reported that the human protein farnesyltransferase (PFT) inhibitor tipifarnib has potent anti-T. cruzi activity by inhibiting the CYP51 enzyme. Furthermore, we have developed analogs that minimize the PFT-inhibitory activity and enhance the CYP51 inhibition. In this paper, we describe the efficacy of the lead tipifarnib analog compared to that of posaconazole in a murine model of T. cruzi infection. The plasma exposure profiles for each compound following a single oral dose in mice and estimated exposure parameters after repeated twice-daily dosing for 20 days are also presented. The lead tipifarnib analog had potent suppressive activity on parasitemia in mice but was unsuccessful at curing mice, whereas posaconazole as well as benznidazole cured 3 of 5 and 4 of 6 mice, respectively. The efficacy results are consistent with posaconazole having substantially higher predicted exposure than that of the tipifarnib analog after repeat twice-daily administration. Further changes to the tipifarnib analogs to reduce plasma clearance are therefore likely to be important. A crystal structure of a trypanosomal CYP51 bound to a tipifarnib analog is reported here and provides new insights to guide structure-based drug design for further optimized compounds.


  • Organizational Affiliation
    • Department of Medicine, University of Washington, Seattle, Washington, USA. fbuckner@u.washington.edu

Macromolecule Content 

  • Total Structure Weight: 209.7 kDa 
  • Atom Count: 14,911 
  • Modeled Residue Count: 1,800 
  • Deposited Residue Count: 1,816 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
sterol 14-alpha demethylase (CYP51)
A, B, C, D
454Trypanosoma bruceiMutation(s): 0 
Gene Names: CYP51Tb11.02.4080
EC: 1.14.13.70
UniProt
Find proteins for Q385E8 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Explore Q385E8 
Go to UniProtKB:  Q385E8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ385E8
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
HEM

Query on HEM



Download:Ideal Coordinates CCD File
E [auth A],
G [auth B],
I [auth C],
K [auth D]
PROTOPORPHYRIN IX CONTAINING FE
C34 H32 Fe N4 O4
KABFMIBPWCXCRK-RGGAHWMASA-L
JKF

Query on JKF



Download:Ideal Coordinates CCD File
F [auth A],
H [auth B],
J [auth C],
L [auth D]
6-[(R)-(4-chlorophenyl)(methoxy)(1-methyl-1H-imidazol-5-yl)methyl]-4-(2,6-difluorophenyl)-1-methylquinolin-2(1H)-one
C28 H22 Cl F2 N3 O2
KVNUNQVIQXLHFU-MUUNZHRXSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.05 Å
  • R-Value Free:  0.243 (Depositor), 0.241 (DCC) 
  • R-Value Work:  0.186 (Depositor), 0.185 (DCC) 
  • R-Value Observed: 0.189 (Depositor) 
Space Group: P 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.722α = 74.47
b = 79.715β = 81.58
c = 117.521γ = 68.05
Software Package:
Software NamePurpose
HKL-2000data collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-07-11
    Type: Initial release
  • Version 1.1: 2012-07-25
    Changes: Database references
  • Version 1.2: 2012-09-05
    Changes: Database references
  • Version 1.3: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description