8E9E

Rat protein farnesyltransferase in complex with FPP and inhibitor 2f


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structure-Guided Discovery of Potent Antifungals that Prevent Ras Signaling by Inhibiting Protein Farnesyltransferase.

Wang, Y.Xu, F.Nichols, C.B.Shi, Y.Hellinga, H.W.Alspaugh, J.A.Distefano, M.D.Beese, L.S.

(2022) J Med Chem 65: 13753-13770

  • DOI: https://doi.org/10.1021/acs.jmedchem.2c00902
  • Primary Citation of Related Structures:  
    7T08, 7T09, 7T0A, 7T0B, 7T0C, 7T0D, 7T0E, 8E9E

  • PubMed Abstract: 

    Infections by fungal pathogens are difficult to treat due to a paucity of antifungals and emerging resistances. Next-generation antifungals therefore are needed urgently. We have developed compounds that prevent farnesylation of Cryptoccoccus neoformans Ras protein by inhibiting protein farnesyltransferase with 3-4 nanomolar affinities. Farnesylation directs Ras to the cell membrane and is required for infectivity of this lethal pathogenic fungus. Our high-affinity compounds inhibit fungal growth with 3-6 micromolar minimum inhibitory concentrations (MICs), 4- to 8-fold better than Fluconazole, an antifungal commonly used in the clinic. Compounds bound with distinct inhibition mechanisms at two alternative, partially overlapping binding sites, accessed via different inhibitor conformations. We showed that antifungal potency depends critically on the selected inhibition mechanism because this determines the efficacy of an inhibitor at low in vivo levels of enzyme and farnesyl substrate. We elucidated how chemical modifications of the antifungals encode desired inhibitor conformation and concomitant inhibitory mechanism.


  • Organizational Affiliation

    Department of Biochemistry, Duke University School of Medicine, Durham, North Carolina27710, United States.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alpha377Rattus norvegicusMutation(s): 0 
Gene Names: Fnta
EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
UniProt
Find proteins for Q04631 (Rattus norvegicus)
Explore Q04631 
Go to UniProtKB:  Q04631
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ04631
Sequence Annotations
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Protein farnesyltransferase subunit beta437Rattus norvegicusMutation(s): 0 
Gene Names: Fntb
EC: 2.5.1.58
UniProt
Find proteins for Q02293 (Rattus norvegicus)
Explore Q02293 
Go to UniProtKB:  Q02293
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ02293
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
XMY (Subject of Investigation/LOI)
Query on XMY

Download Ideal Coordinates CCD File 
K [auth B](5S)-4-({1-[(4-bromophenyl)methyl]-1H-imidazol-5-yl}methyl)-5-butyl-1-[3-(trifluoromethoxy)phenyl]piperazin-2-one
C26 H28 Br F3 N4 O2
GQAHQWQDBPUSHR-QFIPXVFZSA-N
FPP
Query on FPP

Download Ideal Coordinates CCD File 
I [auth B]FARNESYL DIPHOSPHATE
C15 H28 O7 P2
VWFJDQUYCIWHTN-YFVJMOTDSA-N
TRS
Query on TRS

Download Ideal Coordinates CCD File 
C [auth A],
D [auth A],
E [auth A],
M [auth B]
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
ZN
Query on ZN

Download Ideal Coordinates CCD File 
J [auth B]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
L [auth B]
N [auth B]
F [auth A],
G [auth A],
H [auth A],
L [auth B],
N [auth B],
O [auth B],
P [auth B],
Q [auth B],
R [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
FPP BindingDB:  8E9E Kd: 2 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.84 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.176 
  • R-Value Observed: 0.177 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 169.898α = 90
b = 169.898β = 90
c = 69.339γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United States5P01AI104533

Revision History  (Full details and data files)

  • Version 1.0: 2022-10-26
    Type: Initial release
  • Version 1.1: 2022-11-09
    Changes: Database references
  • Version 1.2: 2023-10-18
    Changes: Data collection, Refinement description