4ZT4 | pdb_00004zt4

Trypanosoma brucei methionyl-tRNA synthetase in complex with inhibitorN-(3,5-dichlorobenzyl)-2,2-difluoro-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine (Chem 1708)

• PDB DOI: https://doi.org/10.2210/pdb4ZT4/pdb

• Classification: Ligase/Ligase Inhibitor
• Organism(s): Trypanosoma brucei brucei TREU927
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2015-05-14 Released: 2016-05-04 
• Deposition Author(s): Koh, C.-Y., Hol, W.G.J.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 
  0.225 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.200 (Depositor) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

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

• PubMed: 27627628 
• DOI: https://doi.org/10.1021/acsinfecdis.6b00036
• Primary Citation Related Structures: 
  4ZT2, 4ZT3, 4ZT4, 4ZT5, 4ZT6, 4ZT7


• 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 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.

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Organizational Affiliation: 
• Department of Biochemistry, University of Washington , 1705 N.E. Pacific Street, 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.
Department of Chemistry, Bagley Hall, University of Washington , Seattle, Washington 98195, United States.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 123.83 kDa 
• Atom Count: 8,730 
• Modeled Residue Count: 1,048 
• Deposited Residue Count: 1,084 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Methionyl-tRNA synthetase	A, B	542	Trypanosoma brucei brucei TREU927	Mutation(s): 3  Gene Names: Tb10.70.6470 EC: 6.1.1.10
UniProt
Find proteins for Q38C91 (Trypanosoma brucei brucei (strain 927/4 GUTat10.1)) Explore Q38C91  Go to UniProtKB:  Q38C91

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
4RO	I [auth B]	N-(3,5-dichlorobenzyl)-2,2-difluoro-N'-(1H-imidazo[4,5-b]pyridin-2-yl)propane-1,3-diamine C16 H15 Cl2 F2 N5 MEIIHMGWEAIZIU-UHFFFAOYSA-N
MET	C [auth A]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
SO4	H [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	G [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	D [auth A], E [auth A], F [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CAS	A, B	L-PEPTIDE LINKING	C5 H12 As N O2 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free:  0.225 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.200 (Depositor) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 87.516	α = 90
b = 106.128	β = 90
c = 207.106	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
Coot	model building

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2016-05-04 
Deposition Author(s): Koh, C.-Y., Hol, W.G.J.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	--

Revision History  

• Version 1.0: 2016-05-04
  Type: Initial release
  
• Version 1.1: 2016-10-12
  Changes: Database references
• Version 1.2: 2020-01-15
  Changes: Author supporting evidence, Derived calculations
• Version 1.3: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.4: 2024-11-06
  Changes: Structure summary