4ZT3

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitor N-(3,5-dichlorobenzyl)-N'-(5-fluoro-1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1614)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

5-Fluoroimidazo[4,5-b]pyridine Is a Privileged Fragment That Conveys Bioavailability to Potent Trypanosomal Methionyl-tRNA Synthetase Inhibitors.

Zhang, Z.Koh, C.Y.Ranade, R.M.Shibata, S.Gillespie, J.R.Hulverson, M.A.Huang, W.Nguyen, J.Pendem, N.Gelb, M.H.Verlinde, C.L.Hol, W.G.Buckner, F.S.Fan, E.

(2016) Acs Infect Dis. 2: 399-404

  • DOI: 10.1021/acsinfecdis.6b00036
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Fluorination is a well-known strategy for improving the bioavailability of drug molecules. However, its impact on efficacy is not easily predicted. On the basis of inhibitor-bound protein crystal structures, we found a beneficial fluorination spot fo ...

    Fluorination is a well-known strategy for improving the bioavailability of drug molecules. However, its impact on efficacy is not easily predicted. On the basis of inhibitor-bound protein crystal structures, we found a beneficial fluorination spot for inhibitors targeting methionyl-tRNA synthetase of Trypanosoma brucei. In particular, incorporating 5-fluoroimidazo[4,5-b]pyridine into inhibitors leads to central nervous system bioavailability and maintained or even improved efficacy.


    Organizational Affiliation

    Department of Biochemistry, University of Washington , 1705 N.E. Pacific Street, Seattle, Washington 98195, United States.,Department of Chemistry, Bagley Hall, University of Washington , Seattle, Washington 98195, United States.,Department of Medicine, Division of Allergy and Infectious Diseases, and the Center for Emerging and Re-emerging Infectious Diseases (CERID), University of Washington , 750 Republican Street, Seattle, Washington 98109, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Methionyl-tRNA synthetase
A, B
542Trypanosoma brucei brucei (strain 927/4 GUTat10.1)Mutation(s): 3 
EC: 6.1.1.10
Find proteins for Q38C91 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1))
Go to UniProtKB:  Q38C91
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A, B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
4RQ
Query on 4RQ

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Download CCD File 
B
N-(3,5-dichlorobenzyl)-N'-(5-fluoro-1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine
C16 H16 Cl2 F N5
PLEWLGWDDKXXIA-UHFFFAOYSA-N
 Ligand Interaction
DMS
Query on DMS

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Download CCD File 
A, B
DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
 Ligand Interaction
MET
Query on MET

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Download CCD File 
A
METHIONINE
C5 H11 N O2 S
FFEARJCKVFRZRR-BYPYZUCNSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
CAS
Query on CAS
A, B
L-PEPTIDE LINKINGC5 H12 As N O2 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.249 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 86.696α = 90.00
b = 106.054β = 90.00
c = 207.453γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
Cootmodel building
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of HealthUnited States--

Revision History 

  • Version 1.0: 2016-05-04
    Type: Initial release
  • Version 1.1: 2016-10-12
    Type: Database references