Structure of yeast Sec14p with a picolinamide compound

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 

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This is version 1.3 of the entry. See complete history


Target Identification and Mechanism of Action of Picolinamide and Benzamide Chemotypes with Antifungal Properties.

Pries, V.Nocker, C.Khan, D.Johnen, P.Hong, Z.Tripathi, A.Keller, A.L.Fitz, M.Perruccio, F.Filipuzzi, I.Thavam, S.Aust, T.Riedl, R.Ziegler, S.Bono, F.Schaaf, G.Bankaitis, V.A.Waldmann, H.Hoepfner, D.

(2018) Cell Chem Biol 25: 279-290.e7

  • DOI: https://doi.org/10.1016/j.chembiol.2017.12.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Invasive fungal infections are accompanied by high mortality rates that range up to 90%. At present, only three different compound classes are available for use in the clinic, and these often suffer from low bioavailability, toxicity, and drug resistance. These issues emphasize an urgent need for novel antifungal agents. Herein, we report the identification of chemically versatile benzamide and picolinamide scaffolds with antifungal properties. Chemogenomic profiling and biochemical assays with purified protein identified Sec14p, the major phosphatidylinositol/phosphatidylcholine transfer protein in Saccharomyces cerevisiae, as the sole essential target for these compounds. A functional variomics screen identified resistance-conferring residues that localized to the lipid-binding pocket of Sec14p. Determination of the X-ray co-crystal structure of a Sec14p-compound complex confirmed binding in this cavity and rationalized both the resistance-conferring residues and the observed structure-activity relationships. Taken together, these findings open new avenues for rational compound optimization and development of novel antifungal agents.

  • Organizational Affiliation

    Novartis Institutes for BioMedical Research, Novartis Pharma AG, Forum 1 Novartis Campus, 4056 Basel, Switzerland; Institute of Crop Science and Resource Conservation, Universität Bonn, Karlrobert-Kreiten-Strasse 13, 53113 Bonn, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
SEC14 cytosolic factor312Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SEC14PIT1YMR079WYM9582.04
Find proteins for P24280 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P24280 
Go to UniProtKB:  P24280
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24280
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on C8K

Download Ideal Coordinates CCD File 
B [auth A]~{N}-(1,3-benzodioxol-5-ylmethyl)-5-bromanyl-3-fluoranyl-pyridine-2-carboxamide
C14 H10 Br F N2 O3
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.201 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 88.077α = 90
b = 88.077β = 90
c = 109.254γ = 120
Software Package:
Software NamePurpose
XDSdata reduction
XDSdata scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of HealthUnited StatesGM44530
Robert A. Welch FoundationUnited StatesBE-0017
German Research FoundationGermanySCHA 1274/2-1, SFB 1101/TP A05 and SCHA 1274/4-1
Max Planck SocietyGermany(FP7/2007-2013
European Research CouncilGermany310957
German Research FoundationGermanyBO3588/2-1

Revision History  (Full details and data files)

  • Version 1.0: 2018-01-17
    Type: Initial release
  • Version 1.1: 2018-01-31
    Changes: Author supporting evidence
  • Version 1.2: 2018-03-28
    Changes: Database references
  • Version 1.3: 2024-01-17
    Changes: Data collection, Database references, Refinement description