4CYQ | pdb_00004cyq

Leishmania major N-myristoyltransferase in complex with a hybrid inhibitor (compound 45).

• PDB DOI: https://doi.org/10.2210/pdb4CYQ/pdb

• Classification: TRANSFERASE
• Organism(s): Leishmania major
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2014-04-14 Released: 2014-10-01 
• Deposition Author(s): Hutton, J.A., Goncalves, V., Brannigan, J.A., Paape, D., Waugh, T., Roberts, S.M., Bell, A.S., Wilkinson, A.J., Smith, D.F., Leatherbarrow, R.J., Tate, E.W.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.234 (Depositor), 0.248 (DCC) 
• R-Value Work: 
  0.183 (Depositor) 
• R-Value Observed: 
  0.185 (Depositor) 

Literature

Structure-Based Design of Potent and Selective Leishmania N- Myristoyltransferase Inhibitors.

Hutton, J.A., Goncalves, V., Brannigan, J.A., Paape, D., Wright, M.H., Waugh, T.M., Roberts, S.M., Bell, A.S., Wilkinson, A.J., Smith, D.F., Leatherbarrow, R.J., Tate, E.W.

(2014) J Med Chem 57: 8664

• PubMed: 25238611 
• DOI: https://doi.org/10.1021/jm5011397
• Primary Citation Related Structures: 
  4CYN, 4CYO, 4CYP, 4CYQ


• PubMed Abstract: 
  

  Inhibitors of Leishmania N-myristoyltransferase (NMT), a potential target for the treatment of leishmaniasis, obtained from a high-throughput screen, were resynthesized to validate activity. Crystal structures bound to Leishmania major NMT were obtained, and the active diastereoisomer of one of the inhibitors was identified. On the basis of structural insights, enzyme inhibition was increased 40-fold through hybridization of two distinct binding modes, resulting in novel, highly potent Leishmania donovani NMT inhibitors with good selectivity over the human enzyme.

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Organizational Affiliation: 
• Department of Chemistry, Imperial College London , London SW7 2AZ, U.K.

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 49.07 kDa 
• Atom Count: 3,981 
• Modeled Residue Count: 411 
• Deposited Residue Count: 411 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE	A	411	Leishmania major	Mutation(s): 0  EC: 2.3.1.97
UniProt
Find proteins for Q4Q5S8 (Leishmania major) Explore Q4Q5S8  Go to UniProtKB:  Q4Q5S8

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYA	D [auth A]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-QSGBVPJFSA-N
YAU	C [auth A]	N-{2-chloro-5-[(3S,4R)-1-[(3R)-4-(4-chlorophenyl)-3-hydroxybutanoyl]-4-(hydroxymethyl)pyrrolidin-3-yl]phenyl}-2-(4-fluorophenyl)acetamide C29 H29 Cl2 F N2 O4 LMARVLAZWJAMGJ-NQHRYMMQSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.234 (Depositor), 0.248 (DCC) 
• R-Value Work:  0.183 (Depositor) 
• R-Value Observed: 0.185 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.997	α = 90
b = 92.029	β = 113.1
c = 53.272	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-01 
Deposition Author(s): Hutton, J.A., Goncalves, V., Brannigan, J.A., Paape, D., Waugh, T., Roberts, S.M., Bell, A.S., Wilkinson, A.J., Smith, D.F., Leatherbarrow, R.J., Tate, E.W.

Revision History  

• Version 1.0: 2014-10-01
  Type: Initial release
  
• Version 1.1: 2014-11-05
  Changes: Database references
• Version 1.2: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other