3E37

Protein farnesyltransferase complexed with bisubstrate ethylenediamine scaffold inhibitor 5

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 

wwPDB Validation   3D Report Full Report



Literature

Structural basis for binding and selectivity of antimalarial and anticancer ethylenediamine inhibitors to protein farnesyltransferase.

Hast, M.A., Fletcher, S., Cummings, C.G., Pusateri, E.E., Blaskovich, M.A., Rivas, K., Gelb, M.H., Van Voorhis, W.C., Sebti, S.M., Hamilton, A.D., Beese, L.S.

(2009) Chem Biol 16: 181-192

  • DOI: 10.1016/j.chembiol.2009.01.014
  • Primary Citation of Related Structures:  
    3E32, 3E33, 3E34, 3E37, 3E30

  • PubMed Abstract: 

    • Protein farnesyltransferase (FTase) catalyzes an essential posttranslational lipid modification of more than 60 proteins involved in intracellular signal transduction networks. FTase inhibitors have emerged as a significant target for development of ...

    Protein farnesyltransferase (FTase) catalyzes an essential posttranslational lipid modification of more than 60 proteins involved in intracellular signal transduction networks. FTase inhibitors have emerged as a significant target for development of anticancer therapeutics and, more recently, for the treatment of parasitic diseases caused by protozoan pathogens, including malaria (Plasmodium falciparum). We present the X-ray crystallographic structures of complexes of mammalian FTase with five inhibitors based on an ethylenediamine scaffold, two of which exhibit over 1000-fold selective inhibition of P. falciparum FTase. These structures reveal the dominant determinants in both the inhibitor and enzyme that control binding and selectivity. Comparison to a homology model constructed for the P. falciparum FTase suggests opportunities for further improving selectivity of a new generation of antimalarial inhibitors.

    Organizational Affiliation: 

    Department of Biochemistry, Duke University Medical Center, Box 3711, Durham, NC 27710, USA.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Protein farnesyltransferase/geranylgeranyltransferase type-1 subunit alphaA379Homo sapiensMutation(s): 0 
Gene Names: FNTA
EC: 2.5.1.58 (PDB Primary Data), 2.5.1.59 (PDB Primary Data)
Find proteins for P49354 (Homo sapiens)
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Go to UniProtKB:  P49354
NIH Common Fund Data Resources
PHAROS  P49354
GTEx  ENSG00000168522
Protein Feature View
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  • Reference Sequence
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(by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Protein farnesyltransferase subunit betaB437Homo sapiensMutation(s): 0 
Gene Names: FNTB
EC: 2.5.1.58
Find proteins for P49356 (Homo sapiens)
Explore P49356 
Go to UniProtKB:  P49356
NIH Common Fund Data Resources
PHAROS  P49356
GTEx  ENSG00000257365
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
beta-D-fructofuranose-(2-1)-alpha-D-glucopyranose
C
2 N/A Oligosaccharides Interaction
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ED5
Query on ED5
Download CCD File 
B
tert-butyl 4-({(2-{(4-cyanophenyl)[(1-methyl-1H-imidazol-5-yl)methyl]amino}ethyl)[(2-methylphenyl)sulfonyl]amino}methyl)piperidine-1-carboxylate
C32 H42 N6 O4 S
CHEKEDNUVFBGCF-UHFFFAOYSA-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 %)
ED5IC50:  4050   nM  Binding MOAD
ED5IC50:  4050   nM  BindingDB
Biologically Interesting Molecules (External Reference) 1 Unique
Entity ID: 3
IDChainsNameType/Class2D Diagram3D Interactions
PRD_900003
Query on PRD_900003		CsucroseOligosaccharide /  Nutrient

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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.168 
  • R-Value Observed: 0.169 
  • Space Group: P 61
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 178.386α = 90
b = 178.386β = 90
c = 64.51γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-03-10
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary