7ZGC

Structure of yeast Sec14p with NPPM481


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 

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Ligand Structure Quality Assessment 


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Literature

Mechanisms by Which Small Molecules of Diverse Chemotypes Arrest Sec14 Lipid Transfer Activity.

Chen, X.R.Poudel, L.Hong, Z.Johnen, P.Katti, S.Tripathi, A.Nile, A.H.Green, S.M.Khan, D.Schaaf, G.Bono, F.Bankaitis, V.A.Igumenova, T.I.

(2023) J Biol Chem : 102861-102861

  • DOI: 10.1016/j.jbc.2022.102861
  • Primary Citation of Related Structures:  
    7ZG9, 7ZGA, 7ZGB, 7ZGC, 7ZGD

  • PubMed Abstract: 
  • Phosphatidylinositol (PtdIns) transfer proteins (PITPs) enhance the activities of PtdIns 4-OH kinases that generate signaling pools of PtdIns-4-phosphate. In that capacity, PITPs serve as key regulators of lipid signaling in eukaryotic cells. Although the PITP phospholipid exchange cycle is the engine that stimulates PtdIns 4-OH kinase activities, the underlying mechanism is not understood ...

    Phosphatidylinositol (PtdIns) transfer proteins (PITPs) enhance the activities of PtdIns 4-OH kinases that generate signaling pools of PtdIns-4-phosphate. In that capacity, PITPs serve as key regulators of lipid signaling in eukaryotic cells. Although the PITP phospholipid exchange cycle is the engine that stimulates PtdIns 4-OH kinase activities, the underlying mechanism is not understood. Herein, we apply an integrative structural biology approach to investigate interactions of the yeast PITP Sec14 with small-molecule inhibitors (SMIs) of its phospholipid exchange cycle. Using a combination of X-ray crystallography, solution NMR spectroscopy, and atomistic MD simulations, we dissect how SMIs compete with native Sec14 phospholipid ligands and arrest phospholipid exchange. Moreover, as Sec14 PITPs represent new targets for the development of next-generation antifungal drugs, the structures of Sec14 bound to SMIs of diverse chemotypes reported in this study will provide critical information required for future structure-based design of next-generation lead compounds directed against Sec14 PITPs of virulent fungi.


    Organizational Affiliation

    Department of Biochemistry & Biophysics, Texas A&M University, College Station, Texas USA. Electronic address: Tatyana.Igumenova@ag.tamu.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
SEC14 cytosolic factorA312Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SEC14PIT1YMR079WYM9582.04
UniProt
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
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
IUO (Subject of Investigation/LOI)
Query on IUO

Download Ideal Coordinates CCD File 
B [auth A](4-chloranyl-3-nitro-phenyl)-[4-(2-fluorophenyl)piperazin-1-yl]methanone
C17 H15 Cl F N3 O3
LSPJXCGEFJDMHA-UHFFFAOYSA-N
 Ligand Interaction
PO4
Query on PO4

Download Ideal Coordinates CCD File 
C [auth A]PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.24 Å
  • R-Value Free: 0.211 
  • R-Value Work: 0.184 
  • R-Value Observed: 0.186 
  • Space Group: P 32 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 86.217α = 90
b = 86.217β = 90
c = 109.657γ = 120
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Not funded--

Revision History  (Full details and data files)

  • Version 1.0: 2023-01-25
    Type: Initial release