6EPA

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 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 

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Ligand Structure Quality Assessment 


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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: 10.1021/acs.jmedchem.8b00088
  • Primary Citation of 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) ...

    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.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FI18190p1A187Drosophila melanogasterMutation(s): 1 
Gene Names: frq2Dmel\CG5907frqFrq2-RACG5907Dmel_CG5907Frq2dNCS-1Frq
UniProt
Find proteins for Q9VWX8 (Drosophila melanogaster)
Explore Q9VWX8 
Go to UniProtKB:  Q9VWX8
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BNQ (Subject of Investigation/LOI)
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
 Ligand Interaction
PG0
Query on PG0

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

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

Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
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 
  • R-Value Work: 0.189 
  • R-Value Observed: 0.191 
  • 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