4UCP

CRYSTAL STRUCTURE OF LEISHMANIA MAJOR N-MYRISTOYLTRANSFERASE (NMT) WITH BOUND MYRISTOYL-COA AND A FRAGMENT

• PDB DOI: https://doi.org/10.2210/pdb4UCP/pdb

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


• Deposited: 2014-12-04 Released: 2015-05-13 
• Deposition Author(s): Robinson, D.A., Wyatt, P.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.196 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 

Literature

Identification and Structure Solution of Fragment Hits Against Kinetoplastid N-Myristoyltransferase

Robinson, D.A., Wyatt, P.G.

(2015) Acta Crystallogr Sect F Struct Biol Cryst Commun 71: 586

• PubMed: 25945713 
• DOI: https://doi.org/10.1107/S2053230X15003040
• Primary Citation of Related Structures:  
  4UCM, 4UCN, 4UCP


• PubMed Abstract: 
  

  Trypanosoma brucei N-myristoyltransferase (TbNMT) is an attractive therapeutic target for the treatment of human African trypanosomiasis. Pyrazole sulfonamide (DDD85646), a potent inhibitor of TbNMT, has been identified in previous studies; however, poor central nervous system exposure restricts its use to the haemolymphatic form (stage 1) of the disease. In order to identify new chemical matter, a fragment screen was carried out by ligand-observed NMR spectroscopy, identifying hits that occupy the DDD85646 binding site. Crystal structures of hits from this assay have been obtained in complex with the closely related NMT from Leishmania major, providing a structural starting point for the evolution of novel chemical matter.

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Organizational Affiliation: 

Drug Discovery Unit, College of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, Scotland.

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: 51.71 kDa 
• Atom Count: 3,832 
• Modelled Residue Count: 411 
• Deposited Residue Count: 438 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLYCYLPEPTIDE N-TETRADECANOYLTRANSFERASE	A	438	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MYA	C [auth A]	TETRADECANOYL-COA C35 H62 N7 O17 P3 S DUAFKXOFBZQTQE-QSGBVPJFSA-N
9X3	B [auth A]	N-methyl-1-[3-(morpholin-4-ylmethyl)phenyl]methanamine C13 H20 N2 O JZMYRFZAMCXUIF-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
9X3	Binding MOAD:  4UCP	Kd: 2.00e+5 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.196 
• R-Value Work: 0.170 
• R-Value Observed: 0.171 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 48.501	α = 90
b = 90.889	β = 114.01
c = 53.509	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-05-13 
Deposition Author(s): Robinson, D.A., Wyatt, P.G.

Revision History  

• Version 1.0: 2015-05-13
  Type: Initial release
  
• Version 1.1: 2015-05-20
  Changes: Database references
• Version 1.2: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description