5A28 | pdb_00005a28

Leishmania major N-myristoyltransferase in complex with a chlorophenyl 1,3,4-oxadiazole inhibitor.

• PDB DOI: https://doi.org/10.2210/pdb5A28/pdb

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


• Deposited: 2015-05-15 Released: 2016-03-23 
• Deposition Author(s): Rackham, M.D., Yu, Z., Brannigan, J.A., Heal, W.P., Paape, D., Barker, K.V., Wilkinson, A.J., Smith, D.F., Tate, E.W., Leatherbarrow, R.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free: 
  0.245 (Depositor), 0.241 (DCC) 
• R-Value Work: 
  0.201 (Depositor), 0.195 (DCC) 
• R-Value Observed: 
  0.203 (Depositor) 

Literature

Discovery of High Affinity Inhibitors of Leishmania Donovani N-Myristoyltransferase.

Rackham, M.D., Yu, Z., Brannigan, J.A., Heal, W.P., Paape, D., Barker, K.V., Wilkinson, A.J., Smith, D.F., Leatherbarrow, R.J., Tate, E.W.

(2015) Medchemcomm 6: 1761

• PubMed: 26962429 
• DOI: https://doi.org/10.1039/c5md00241a
• Primary Citation Related Structures: 
  5A27, 5A28


• PubMed Abstract: 
  

  N -Myristoyltransferase (NMT) is a potential drug target in Leishmania parasites. Scaffold-hopping from published inhibitors yielded the serendipitous discovery of a chemotype selective for Leishmania donovani NMT; development led to high affinity inhibitors with excellent ligand efficiency. The binding mode was characterised by crystallography and provides a structural rationale for selectivity.

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Organizational Affiliation: 
• Department of Chemistry , Imperial College London , South Kensington Campus , London , SW7 2AZ , UK . Email: [e-mail] ; Tel: [phone].
Structural Biology Laboratory , Department of Chemistry , University of York , York , YO10 5DD , UK.
Department of Biology , University of York , York , YO10 5DD , UK.

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: 48.91 kDa 
• Atom Count: 4,018 
• 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	B [auth A]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-QSGBVPJFSA-N
TUQ	C [auth A]	4-(4-chloro-2-{5-[(trimethyl-1H-pyrazol-4-yl)methyl]-1,3,4-oxadiazol-2-yl}phenoxy)piperidine C20 H24 Cl N5 O2 AYWNZLSZEHOECC-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.48 Å
• R-Value Free:  0.245 (Depositor), 0.241 (DCC) 
• R-Value Work:  0.201 (Depositor), 0.195 (DCC) 
• R-Value Observed: 0.203 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.447	α = 90
b = 92.161	β = 113.79
c = 53.461	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-03-23 
Deposition Author(s): Rackham, M.D., Yu, Z., Brannigan, J.A., Heal, W.P., Paape, D., Barker, K.V., Wilkinson, A.J., Smith, D.F., Tate, E.W., Leatherbarrow, R.J.

Revision History  

• Version 1.0: 2016-03-23
  Type: Initial release
  
• Version 1.1: 2024-05-08
  Changes: Data collection, Database references, Derived calculations, Other