1IYL

Crystal Structure of Candida albicans N-myristoyltransferase with Non-peptidic Inhibitor

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.288 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history. 


Literature

Crystal Structures of Candida albicans N-Myristoyltransferase with Two Distinct Inhibitors

Sogabe, S., Masubuchi, M., Sakata, K., Fukami, T.A., Morikami, K., Shiratori, Y., Ebiike, H., Kawasaki, K., Aoki, Y., Shimma, N., D'Arcy, A., Winkler, F.K., Banner, D.W., Ohtsuka, T.

(2002) Chem Biol 9: 1119-1128

  • DOI: 10.1016/s1074-5521(02)00240-5
  • Primary Citation of Related Structures:  
    1IYK, 1IYL

  • PubMed Abstract: 

    • Myristoyl-CoA:protein N-myristoyltransferase (Nmt) is a monomeric enzyme that catalyzes the transfer of the fatty acid myristate from myristoyl-CoA to the N-terminal glycine residue of a variety of eukaryotic and viral proteins. Genetic and biochemical studies have established that Nmt is an attractive target for antifungal drugs ...

    Myristoyl-CoA:protein N-myristoyltransferase (Nmt) is a monomeric enzyme that catalyzes the transfer of the fatty acid myristate from myristoyl-CoA to the N-terminal glycine residue of a variety of eukaryotic and viral proteins. Genetic and biochemical studies have established that Nmt is an attractive target for antifungal drugs. We present here crystal structures of C. albicans Nmt complexed with two classes of inhibitor competitive for peptide substrates. One is a peptidic inhibitor designed from the peptide substrate; the other is a nonpeptidic inhibitor having a benzofuran core. Both inhibitors are bound into the same binding groove, generated by some structural rearrangements of the enzyme, with the peptidic inhibitor showing a substrate-like binding mode and the nonpeptidic inhibitor binding differently. Further, site-directed mutagenesis for C. albicans Nmt has been utilized in order to define explicitly which amino acids are critical for inhibitor binding. The results suggest that the enzyme has some degree of flexibility for substrate binding and provide valuable information for inhibitor design.

    Organizational Affiliation: 

    Nippon Roche Research Center, 200 Kajiwara, Kamakura, Kanagawa 247-8530, Japan. satoshi.sogabe@roche.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Myristoyl-CoA:Protein N-MyristoyltransferaseA, B, C, D392Candida albicansMutation(s): 0 
EC: 2.3.1.97
UniProt
Find proteins for P30418 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Explore P30418 
Go to UniProtKB:  P30418
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP30418
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R64
Query on R64
Download Ideal Coordinates CCD File 
E [auth A],
F [auth B],
G [auth C]		(1-METHYL-1H-IMIDAZOL-2-YL)-(3-METHYL-4-{3-[(PYRIDIN-3-YLMETHYL)-AMINO]-PROPOXY}-BENZOFURAN-2-YL)-METHANONE
C23 H24 N4 O3
VZBQJKIOAOUYJL-UHFFFAOYSA-N		 Ligand Interaction
Binding Affinity Annotations 
IDSourceBinding Affinity
R64 PDBBind:  1IYL IC50: 1 (nM) from 1 assay(s)
BindingDB:  1IYL IC50: 1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.284 
  • R-Value Observed: 0.288 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.277α = 90
b = 96.885β = 90
c = 269.277γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNXrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-12-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance