6EPA | pdb_00006epa

Structure of dNCS-1 bound to the NCS-1/Ric8a protein/protein interaction regulator IGS-1.76


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free: 
    0.232 (Depositor), 0.245 (DCC) 
  • R-Value Work: 
    0.189 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 
    0.191 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment 


This is version 1.1 of the entry. See complete history

Literature

Deciphering the Inhibition of the Neuronal Calcium Sensor 1 and the Guanine Exchange Factor Ric8a with a Small Phenothiazine Molecule for the Rational Generation of Therapeutic Synapse Function Regulators.

Roca, C.Martinez-Gonzalez, L.Daniel-Mozo, M.Sastre, J.Infantes, L.Mansilla, A.Chaves-Sanjuan, A.Gonzalez-Rubio, J.M.Gil, C.Canada, F.J.Martinez, A.Sanchez-Barrena, M.J.Campillo, N.E.

(2018) J Med Chem 61: 5910-5921

  • DOI: https://doi.org/10.1021/acs.jmedchem.8b00088
  • Primary Citation Related Structures: 
    6EPA

  • PubMed Abstract: 

    Protein-protein interactions (PPIs) are known to play an essential role between the neuronal calcium sensor 1 (NCS-1) and the guanine exchange factor Ric8a to regulate synapse function, emerging as a druggable interface for synaptopathies such as the fragile X syndrome (FXS). Recently, the phenothiazine FD44 has been identified as an inhibitor of this PPI, decreasing the abnormally high synapse number and enhancing associative learning in a FXS animal model. Here, we have integrated advanced experimental and computational studies to obtain important structural insights into Drosophila NCS-1/FD44 recognition to understand the basis of its affinity and specificity and generate improved PPI regulators. This has allowed the identification of a new small drug-like molecule, IGS-1.76, which efficiently inhibits the human NCS-1/Ric8a complex with improved binding potency. The crystal structure of the Drosophila NCS-1/IGS-1.76 complex demonstrates that the new inhibitor, although chemically different from FD44, shares the same mechanism of action and constitutes a new hit candidate for FXS.


  • Organizational Affiliation
    • Centro de Investigaciones Biológicas-CSIC , Ramiro de Maeztu 9 , 28040 Madrid , Spain.

Macromolecule Content 

  • Total Structure Weight: 22.54 kDa 
  • Atom Count: 1,753 
  • Modeled Residue Count: 183 
  • Deposited Residue Count: 187 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
FI18190p1187Drosophila melanogasterMutation(s): 1 
Gene Names: Frq2Dmel\CG5907Frqfrq2Frq2-RACG5907Dmel_CG5907
UniProt
Find proteins for Q9VWX8 (Drosophila melanogaster)
Explore Q9VWX8 
Go to UniProtKB:  Q9VWX8
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9VWX8
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BNQ

Query on BNQ



Download:Ideal Coordinates CCD File
E [auth A]~{N}-(1,3-benzothiazol-2-yl)-3,3-diphenyl-propanamide
C22 H18 N2 O S
GYQWKTIZRYVFEM-UHFFFAOYSA-N
PG0

Query on PG0



Download:Ideal Coordinates CCD File
F [auth A]2-(2-METHOXYETHOXY)ETHANOL
C5 H12 O3
SBASXUCJHJRPEV-UHFFFAOYSA-N
CA

Query on CA



Download:Ideal Coordinates CCD File
B [auth A],
C [auth A],
D [auth A]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NA

Query on NA



Download:Ideal Coordinates CCD File
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
BNQ BindingDB:  6EPA Kd: 1130 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.82 Å
  • R-Value Free:  0.232 (Depositor), 0.245 (DCC) 
  • R-Value Work:  0.189 (Depositor), 0.197 (DCC) 
  • R-Value Observed: 0.191 (Depositor) 
Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.843α = 90
b = 55.456β = 90
c = 61.259γ = 90
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
Spanish Ministry of Economy and CompetitivenessSpainBIO2011-28184-C02-02
Spanish Ministry of Economy and CompetitivenessSpainBFU2014-59796-R
Spanish Ministry of Economy and CompetitivenessSpainRYC-2008-03449
European Commission - InstructSpainR&D Pilot Project APPID 99

Revision History  (Full details and data files)

  • Version 1.0: 2018-08-29
    Type: Initial release
  • Version 1.1: 2024-01-17
    Changes: Data collection, Database references, Derived calculations, Refinement description