4Q4R

tRNA-Guanine Transglycosylase (TGT) in Complex with 2-{[2-(Morpholin-4-yl)ethyl]amino}-1H,7H,8H-imidazo[4,5-g]quinazolin-8-one


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.448 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.136 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Beyond Affinity: Enthalpy-Entropy Factorization Unravels Complexity of a Flat Structure-Activity Relationship for Inhibition of a tRNA-Modifying Enzyme.

Neeb, M.Betz, M.Heine, A.Barandun, L.J.Hohn, C.Diederich, F.Klebe, G.

(2014) J.Med.Chem. 57: 5566-5578

  • DOI: 10.1021/jm5006868
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lead optimization focuses on binding-affinity improvement. If a flat structure-activity relationship is detected, usually optimization strategies are abolished as unattractive. Nonetheless, as affinity is composed of an enthalpic and entropic contrib ...

    Lead optimization focuses on binding-affinity improvement. If a flat structure-activity relationship is detected, usually optimization strategies are abolished as unattractive. Nonetheless, as affinity is composed of an enthalpic and entropic contribution, factorization of both can unravel the complexity of a flat, on first sight tedious SAR. In such cases, the binding free energy of different ligands can be rather similar, but it can factorize into enthalpy and entropy distinctly. We investigated the thermodynamic signature of two classes of lin-benzopurines binding to tRNA-guanine transglycosylase. While the differences are hardly visible in the free energy, they involve striking enthalpic and entropic changes. Analyzing thermodynamics along with structural features revealed that one ligand set binds to the protein without inducing significant changes compared to the apo structure; however, the second series provokes complex adaptation, leading to a conformation similar to the substrate-bound state. In the latter state, a cross-talk between two pockets is suggested.


    Organizational Affiliation

    Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Queuine tRNA-ribosyltransferase
A
386Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4)Mutation(s): 0 
Gene Names: tgt
EC: 2.4.2.29
Find proteins for P28720 (Zymomonas mobilis subsp. mobilis (strain ATCC 31821 / ZM4 / CP4))
Go to UniProtKB:  P28720
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
SQO
Query on SQO

Download SDF File 
Download CCD File 
A
2-{[2-(4-Morpholinyl)ethyl]amino}-1,7-dihydro-8H-imidazo[4,5-g]quinazolin-8-one
C15 H18 N6 O2
IQPSZZDLHUVVGO-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
SQOKd: 369 nM BINDINGMOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.448 Å
  • R-Value Free: 0.172 
  • R-Value Work: 0.136 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 89.941α = 90.00
b = 64.837β = 93.14
c = 70.756γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
PHASERphasing
MAR345dtbdata collection
HKL-2000data scaling
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2014-07-09
    Type: Initial release
  • Version 1.1: 2014-07-23
    Type: Database references