9T0H | pdb_00009t0h

NCS-1 bound to a FDA-approved drug


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free: 
    0.255 (Depositor), 0.254 (DCC) 
  • R-Value Work: 
    0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 
    0.213 (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

An AI-based approach accelerates the discovery of protein-protein interaction modulators targeting NCS-1.

Gonzalez-Garcia, E.Miro-Rodriguez, C.Ulzurrun, E.Toledano, O.Perez-Suarez, S.Aguado, L.Sanchez-Barrena, M.J.Mansilla, A.Naveiro, R.Campillo, N.E.

(2026) Eur J Med Chem 309: 118739-118739

  • DOI: https://doi.org/10.1016/j.ejmech.2026.118739
  • Primary Citation Related Structures: 
    9T0H

  • PubMed Abstract: 

    Drug repurposing is an efficient strategy to accelerate the identification of therapeutic compounds by finding new uses for existing drugs. Here, we leveraged artificial intelligence (AI) to optimize this process and discover protein-protein interaction (PPI) modulators targeting the Neuronal Calcium Sensor 1. AI models were trained on large datasets of known PPIs, protein structures, and small molecular graphs to predict binding score. Using virtual screening of an FDA-approved drug library, the models generated a prioritized list of candidates. The most promising compounds were selected for experimental validation. This integrated approach efficiently reduced experimental workload, time, and cost, leading to the identification of dipyridamole as a selective modulator of the interaction between NCS-1 and the dopamine D 2 receptor. The crystal structure of NCS-1 in complex with dipyridamole elucidates its mechanism of modulation. Our findings highlight the potential of AI to streamline and accelerate the discovery of novel therapeutic PPI modulators.


  • Organizational Affiliation
    • Institute for Complex Molecular Systems, Eindhoven University of Technology, Eindhoven, North Brabant, The Netherlands.

Macromolecule Content 

  • Total Structure Weight: 21.01 kDa 
  • Atom Count: 1,628 
  • Modeled Residue Count: 166 
  • Deposited Residue Count: 170 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Neuronal calcium sensor 1A [auth B]170Homo sapiensMutation(s): 0 
Gene Names: NCS1FLUPFREQ
UniProt & NIH Common Fund Data Resources
Find proteins for P62166 (Homo sapiens)
Explore P62166 
Go to UniProtKB:  P62166
PHAROS:  P62166
GTEx:  ENSG00000107130 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP62166
Sequence Annotations
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Reference Sequence

Small Molecules

Ligands 6 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
H9F
(Subject of Investigation/LOI)

Query on H9F



Download:Ideal Coordinates CCD File
G [auth B]2-[[2-[bis(2-hydroxyethyl)amino]-4,8-di(piperidin-1-yl)pyrimido[5,4-d]pyrimidin-6-yl]-(2-hydroxyethyl)amino]ethanol
C24 H40 N8 O4
IZEKFCXSFNUWAM-UHFFFAOYSA-N
P6G

Query on P6G



Download:Ideal Coordinates CCD File
F [auth B]HEXAETHYLENE GLYCOL
C12 H26 O7
IIRDTKBZINWQAW-UHFFFAOYSA-N
PEG

Query on PEG



Download:Ideal Coordinates CCD File
E [auth B]DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
EOH

Query on EOH



Download:Ideal Coordinates CCD File
H [auth B],
I [auth B]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
CA

Query on CA



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

Query on NA



Download:Ideal Coordinates CCD File
J [auth B],
K [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.91 Å
  • R-Value Free:  0.255 (Depositor), 0.254 (DCC) 
  • R-Value Work:  0.210 (Depositor), 0.210 (DCC) 
  • R-Value Observed: 0.213 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 45.327α = 90
b = 103.021β = 90
c = 76.294γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Spanish Ministry of Science, Innovation, and UniversitiesSpainPID2022-137331OB-C31

Revision History  (Full details and data files)

  • Version 1.0: 2026-03-11
    Type: Initial release
  • Version 1.1: 2026-03-18
    Changes: Database references