1IYL

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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.284 

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

  • Primary Citation of Related Structures:  

  • 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 biochemic ...

    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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Myristoyl-CoA:Protein N-Myristoyltransferase
A, B, C, D
392Candida albicans (strain SC5314 / ATCC MYA-2876)Mutation(s): 0 
Gene Names: NMT1
EC: 2.3.1.97
Find proteins for P30418 (Candida albicans (strain SC5314 / ATCC MYA-2876))
Go to Gene View: NMT1
Go to UniProtKB:  P30418
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
R64
Query on R64
Download SDF File 
Download CCD File 
A, B, 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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
R64IC50: 1 nM (100) BINDINGDB
R64IC50: 1 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.366 
  • R-Value Work: 0.284 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 93.277α = 90.00
b = 96.885β = 90.00
c = 269.277γ = 90.00
Software Package:
Software NamePurpose
AMoREphasing
DENZOdata reduction
CNXrefinement
SCALEPACKdata scaling

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

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