6QDD | pdb_00006qdd

Leishmania major N-myristoyltransferase in complex with thienopyrimidine inhibitor IMP-0000105

• PDB DOI: https://doi.org/10.2210/pdb6QDD/pdb

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


• Deposited: 2019-01-01 Released: 2020-05-06 
• Deposition Author(s): Brannigan, J.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 
  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 
  0.183 (Depositor) 

Literature

Novel Thienopyrimidine Inhibitors of Leishmania N -Myristoyltransferase with On-Target Activity in Intracellular Amastigotes.

Bell, A.S., Yu, Z., Hutton, J.A., Wright, M.H., Brannigan, J.A., Paape, D., Roberts, S.M., Sutherell, C.L., Ritzefeld, M., Wilkinson, A.J., Smith, D.F., Leatherbarrow, R.J., Tate, E.W.

(2020) J Med Chem 63: 7740-7765

• PubMed: 32575985 
• DOI: https://doi.org/10.1021/acs.jmedchem.0c00570
• Primary Citation Related Structures: 
  6QD9, 6QDA, 6QDB, 6QDC, 6QDD, 6QDE, 6QDF, 6QDG, 6QDH


• PubMed Abstract: 
  

  The leishmaniases, caused by Leishmania species of protozoan parasites, are neglected tropical diseases with millions of cases worldwide. Current therapeutic approaches are limited by toxicity, resistance, and cost. N -Myristoyltransferase (NMT), an enzyme ubiquitous and essential in all eukaryotes, has been validated via genetic and pharmacological methods as a promising anti-leishmanial target. Here we describe a comprehensive structure-activity relationship (SAR) study of a thienopyrimidine series previously identified in a high-throughput screen against Leishmania NMT, across 68 compounds in enzyme- and cell-based assay formats. Using a chemical tagging target engagement biomarker assay, we identify the first inhibitor in this series with on-target NMT activity in leishmania parasites. Furthermore, crystal structure analyses of 12 derivatives in complex with Leishmania major NMT revealed key factors important for future structure-guided optimization delivering IMP-105 ( 43 ), a compound with modest activity against Leishmania donovani intracellular amastigotes and excellent selectivity (>660-fold) for Leishmania NMT over human NMTs.

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Organizational Affiliation: 
• Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, London, U.K. W12 0BZ.
School of Chemistry, University of Leeds, Leeds, U.K. LS2 9JT.
Structural Biology Laboratory, York Biomedical Research Institute, Department of Chemistry, University of York, York, U.K. YO10 5DD.
Centre for Immunology and Infection, York Biomedical Research Institute, Department of Biology, University of York, York, U.K. YO10 5NG.

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 50.02 kDa 
• Atom Count: 3,948 
• Modeled Residue Count: 411 
• Deposited Residue Count: 421 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycylpeptide N-tetradecanoyltransferase	A	421	Leishmania major	Mutation(s): 0  Gene Names: NMT, LMJF_32_0080 EC: 2.3.1.97
UniProt
Find proteins for Q4Q5S8 (Leishmania major) Explore Q4Q5S8  Go to UniProtKB:  Q4Q5S8

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYA	B [auth A]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-QSGBVPJFSA-N
HXW	E [auth A]	2-[(2~{S})-1-[2-[methyl-(1-methylpiperidin-4-yl)amino]thieno[3,2-d]pyrimidin-4-yl]-2,3-dihydropyrrol-2-yl]ethanenitrile C19 H24 N6 S ZMXVLDNFPUUWQK-HNNXBMFYSA-N
DMS	C [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
MG	D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free:  0.223 (Depositor), 0.224 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.181 (DCC) 
• R-Value Observed: 0.183 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.154	α = 90
b = 90.849	β = 112.79
c = 53.263	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
SCALA	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-05-06 
Deposition Author(s): Brannigan, J.A.

Revision History  

• Version 1.0: 2020-05-06
  Type: Initial release
  
• Version 1.1: 2020-12-02
  Changes: Database references
• Version 1.2: 2024-05-15
  Changes: Data collection, Database references