3HXE

Engineered RabGGTase in complex with a peptidomimetic inhibitor (compound 37)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.154 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Design, synthesis, and characterization of Peptide-based rab geranylgeranyl transferase inhibitors

Tan, K.T.Guiu-Rozas, E.Bon, R.S.Guo, Z.Delon, C.Wetzel, S.Arndt, S.Alexandrov, K.Waldmann, H.Goody, R.S.Wu, Y.W.Blankenfeldt, W.

(2009) J.Med.Chem. 52: 8025-8037

  • DOI: 10.1021/jm901117d
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Rab geranylgeranyl transferase (RabGGTase) catalyzes the attachment of geranylgeranyl isoprenoids to Rab guanine triphosphatases, which are key regulators in vesicular transport. Because geranylgeranylation is required for proper function and overexp ...

    Rab geranylgeranyl transferase (RabGGTase) catalyzes the attachment of geranylgeranyl isoprenoids to Rab guanine triphosphatases, which are key regulators in vesicular transport. Because geranylgeranylation is required for proper function and overexpression of Rabs has been observed in various cancers, RabGGTase may be a target for novel therapeutics. The development of selective inhibitors is, however, difficult because two related enzymes involved in other cellular processes exist in eukaryotes and because RabGGTase recognizes protein substrates indirectly, resulting in relaxed specificity. We report the synthesis of a peptidic library based on the farnesyl transferase inhibitor pepticinnamin E. Of 469 compounds investigated, several were identified as selective for RabGGTase with low micromolar IC(50) values. The compounds were not generally cytotoxic and inhibited Rab isoprenylation in COS-7 cells. Crystal structure analysis revealed that selective inhibitors interact with a tunnel unique to RabGGTase, implying that this structural motif is an attractive target for improved RabGGTase inhibitors.


    Organizational Affiliation

    Department of Chemical Biology, Biochemistry, Max Planck Institute of Molecular Physiology,Otto-Hahn-Strassse 11, 44227 Dortmund, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Geranylgeranyl transferase type-2 subunit alpha
A
331Rattus norvegicusMutation(s): 0 
Gene Names: Rabggta (Ggta)
EC: 2.5.1.60
Find proteins for Q08602 (Rattus norvegicus)
Go to UniProtKB:  Q08602
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Geranylgeranyl transferase type-2 subunit beta
B
331Rattus norvegicusMutation(s): 0 
Gene Names: Rabggtb (Ggtb)
EC: 2.5.1.60
Find proteins for Q08603 (Rattus norvegicus)
Go to UniProtKB:  Q08603
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BD8
Query on BD8

Download SDF File 
Download CCD File 
B
N-undecanoyl-L-histidyl-L-phenylalanyl-N-methyl-N-(2-pyridin-2-ylethyl)-L-tyrosinamide
C43 H57 N7 O5
KGRSUMUKTYCXCP-IGMOWHQGSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
BD8IC50: 4700 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.215 
  • R-Value Work: 0.154 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.122α = 90.00
b = 90.826β = 90.00
c = 114.727γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
XDSdata reduction
XSCALEdata scaling
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-09-08
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-02-13
    Type: Refinement description
  • Version 1.3: 2017-07-26
    Type: Refinement description, Source and taxonomy