2R2L

Structure of Farnesyl Protein Transferase bound to PB-93


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Efficacy, pharmacokinetics, and metabolism of tetrahydroquinoline inhibitors of Plasmodium falciparum protein farnesyltransferase.

Van Voorhis, W.C.Rivas, K.L.Bendale, P.Nallan, L.Horney, C.Barrett, L.K.Bauer, K.D.Smart, B.P.Ankala, S.Hucke, O.Verlinde, C.L.Chakrabarti, D.Strickland, C.Yokoyama, K.Buckner, F.S.Hamilton, A.D.Williams, D.K.Lombardo, L.J.Floyd, D.Gelb, M.H.

(2007) Antimicrob Agents Chemother 51: 3659-3671

  • DOI: 10.1128/AAC.00246-07
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • New antimalarials are urgently needed. We have shown that tetrahydroquinoline (THQ) protein farnesyltransferase (PFT) inhibitors (PFTIs) are effective against the Plasmodium falciparum PFT and are effective at killing P. falciparum in vitro. Previous ...

    New antimalarials are urgently needed. We have shown that tetrahydroquinoline (THQ) protein farnesyltransferase (PFT) inhibitors (PFTIs) are effective against the Plasmodium falciparum PFT and are effective at killing P. falciparum in vitro. Previously described THQ PFTIs had limitations of poor oral bioavailability and rapid clearance from the circulation of rodents. In this paper, we validate both the Caco-2 cell permeability model for predicting THQ intestinal absorption and the in vitro liver microsome model for predicting THQ clearance in vivo. Incremental improvements in efficacy, oral absorption, and clearance rate were monitored by in vitro tests; and these tests were followed up with in vivo absorption, distribution, metabolism, and excretion studies. One compound, PB-93, achieved cure when it was given orally to P. berghei-infected rats every 8 h for a total of 72 h. However, PB-93 was rapidly cleared, and dosing every 12 h failed to cure the rats. Thus, the in vivo results corroborate the in vitro pharmacodynamics and demonstrate that 72 h of continuous high-level exposure to PFTIs is necessary to kill plasmodia. The metabolism of PB-93 was demonstrated by a novel technique that relied on double labeling with a radiolabel and heavy isotopes combined with radiometric liquid chromatography and mass spectrometry. The major liver microsome metabolite of PB-93 has the PFT Zn-binding N-methyl-imidazole removed; this metabolite is inactive in blocking PFT function. By solving the X-ray crystal structure of PB-93 bound to rat PFT, a model of PB-93 bound to malarial PFT was constructed. This model suggests areas of the THQ PFTIs that can be modified to retain efficacy and protect the Zn-binding N-methyl-imidazole from dealkylation.


    Organizational Affiliation

    Department of Medicine, University of Washington, Room I-104-E, Health Sciences Building, Seattle, WA 98195-7185, USA. wesley@u.washington.edu



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Farnesyltransferase subunit alpha
A
315Rattus norvegicusMutation(s): 0 
Gene Names: FntarCG_42999
Find proteins for Q5RKJ4 (Rattus norvegicus)
Go to UniProtKB:  Q5RKJ4

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Farnesyltransferase subunit beta
B
401Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
EC: 2.5.1.58
Find proteins for Q02293 (Rattus norvegicus)
Go to UniProtKB:  Q02293
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PB9
Query on PB9

Download CCD File 
B
methyl 4-{[{(3S)-6-cyano-1-[(1-methyl-1H-imidazol-5-yl)methyl]-1,2,3,4-tetrahydroquinolin-3-yl}(pyridin-2-ylsulfonyl)amino]methyl}piperidine-1-carboxylate
C28 H33 N7 O4 S
BRIVIXLMMUIBJY-DEOSSOPVSA-N
 Ligand Interaction
FPP
Query on FPP

Download CCD File 
B
FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
 Ligand Interaction
ZN
Query on ZN

Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
PB9IC50:  0.5799999833106995   nM  Binding MOAD
PB9IC50:  1   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.23 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.189 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 171.614α = 90
b = 171.614β = 90
c = 69.155γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
PDB_EXTRACTdata extraction
JDirectordata collection
HKL-2000data reduction
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-03-11
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-10-25
    Changes: Refinement description