9GU6 | pdb_00009gu6

NCS-1 bound to FDA ligand 3

PDB DOI: https://doi.org/10.2210/pdb9GU6/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Homo sapiens
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2024-09-19 Released: 2025-11-19
Deposition Author(s): Munoz-Reyes, D., Sanchez-Barrena, M.J.
Funding Organization(s): Ministerio de Ciencia e Innovacion (MCIN)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.93 Å
R-Value Free:
0.256 (Depositor), 0.258 (DCC)
R-Value Work:
0.219 (Depositor), 0.220 (DCC)
R-Value Observed:
0.221 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

FDA Drug Repurposing Uncovers Modulators of Dopamine D 2 Receptor Localization via Disruption of the NCS-1 Interaction.

Munoz-Reyes, D., Aguado, L., Arroyo-Urea, S., Requena, C., Perez-Suarez, S., Sanchez-Yepes, S., Argerich, J., Miro-Rodriguez, C., Ulzurrun, E., Rodriguez-Martin, E., Garcia-Nafria, J., Campillo, N.E., Mansilla, A., Sanchez-Barrena, M.J.

(2025) J Med Chem 68: 23993-24010

PubMed: 41211723 Search on PubMed
DOI: https://doi.org/10.1021/acs.jmedchem.5c01626
Primary Citation Related Structures:
9GTO, 9GU6, 9GU8

PubMed Abstract:
Dopamine D ₂ receptor (D ₂R) regulates key aspects of motor control, cognition, and reward. Its function depends not only on ligand binding and signaling efficacy but also on the dynamic control of receptor localization at the cell surface. Neuronal calcium sensor 1 (NCS-1) interacts with D ₂R in a Ca ²⁺-dependent manner. Using in vitro and cellular assays, we found that NCS-1 promotes D ₂R trafficking to the plasma membrane through active exocytosis while preserving canonical receptor pharmacology. A screen of FDA-approved drugs identified protein-protein interaction (PPI) modulators targeting the NCS-1/D ₂R interface. Azilsartan medoxomil, atorvastatin, and vilazodone disrupt this interaction, reducing D ₂R surface expression. Structural studies revealed that these compounds target NCS-1, overlap the D ₂R binding site, and perturb the dynamics of the regulatory helix H10. These findings reveal an unexploited intracellular mechanism to modulate D ₂R function via PPI modulation, offering a novel strategy to fine-tune dopaminergic tone beyond receptor blockade or direct agonism.

Organizational Affiliation

Department of Crystallography and Structural Biology, Institute of Physical-Chemistry "Blas Cabrera", CSIC, Serrano 119, 28006 Madrid, Spain.

Macromolecule Content

Total Structure Weight: 93.97 kDa
Atom Count: 6,894
Modeled Residue Count: 724
Deposited Residue Count: 760
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Neuronal calcium sensor 1	A [auth B], B [auth D], C [auth F], D [auth H]	190	Homo sapiens	Mutation(s): 0 Gene Names: NCS1, FLUP, FREQ
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 Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62166
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
117 (Subject of Investigation/LOI) Query on 117 Download:Ideal Coordinates CCD File SDF format, chain H [auth B] SDF format, chain I [auth B] SDF format, chain JA [auth F] SDF format, chain TA [auth H] SDF format, chain W [auth D] SDF format, chain X [auth D] MOL2 format, chain H [auth B] MOL2 format, chain I [auth B] MOL2 format, chain JA [auth F] MOL2 format, chain TA [auth H] MOL2 format, chain W [auth D] MOL2 format, chain X [auth D] mmCIF format, chain H [auth B] mmCIF format, chain I [auth B] mmCIF format, chain JA [auth F] mmCIF format, chain TA [auth H] mmCIF format, chain W [auth D] mmCIF format, chain X [auth D]	H [auth B] I [auth B] JA [auth F] TA [auth H] W [auth D] H [auth B], I [auth B], JA [auth F], TA [auth H], W [auth D], X [auth D]	7-[2-(4-FLUORO-PHENYL)-5-ISOPROPYL-3-PHENYL-4-PHENYLCARBAMOYL-PYRROL-1-YL]- 3,5-DIHYDROXY-HEPTANOIC ACID C₃₃ H₃₅ F N₂ O₅ XUKUURHRXDUEBC-KAYWLYCHSA-N		Interactions Focus chain H [auth B] Focus chain I [auth B] Focus chain JA [auth F] Focus chain TA [auth H] Focus chain W [auth D] Focus chain X [auth D] Interactions & Density Focus chain H [auth B] Focus chain I [auth B] Focus chain JA [auth F] Focus chain TA [auth H] Focus chain W [auth D] Focus chain X [auth D]
SIN Query on SIN Download:Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain MA [auth F] SDF format, chain NA [auth F] SDF format, chain O [auth B] SDF format, chain WA [auth H] SDF format, chain XA [auth H] SDF format, chain YA [auth H] SDF format, chain ZA [auth H] SDF format, chain N [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain MA [auth F] MOL2 format, chain NA [auth F] MOL2 format, chain O [auth B] MOL2 format, chain WA [auth H] MOL2 format, chain XA [auth H] MOL2 format, chain YA [auth H] MOL2 format, chain ZA [auth H] MOL2 format, chain N [auth B] mmCIF format, chain BA [auth D] mmCIF format, chain CA [auth D] mmCIF format, chain MA [auth F] mmCIF format, chain NA [auth F] mmCIF format, chain O [auth B] mmCIF format, chain WA [auth H] mmCIF format, chain XA [auth H] mmCIF format, chain YA [auth H] mmCIF format, chain ZA [auth H] mmCIF format, chain N [auth B]	BA [auth D] CA [auth D] MA [auth F] N [auth B] NA [auth F] BA [auth D], CA [auth D], MA [auth F], N [auth B], NA [auth F], O [auth B], WA [auth H], XA [auth H], YA [auth H], ZA [auth H]	SUCCINIC ACID C₄ H₆ O₄ KDYFGRWQOYBRFD-UHFFFAOYSA-N		Interactions Focus chain BA [auth D] Focus chain CA [auth D] Focus chain MA [auth F] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain WA [auth H] Focus chain XA [auth H] Focus chain YA [auth H] Focus chain ZA [auth H] Interactions & Density Focus chain BA [auth D] Focus chain CA [auth D] Focus chain MA [auth F] Focus chain N [auth B] Focus chain NA [auth F] Focus chain O [auth B] Focus chain WA [auth H] Focus chain XA [auth H] Focus chain YA [auth H] Focus chain ZA [auth H]
MLI Query on MLI Download:Ideal Coordinates CCD File SDF format, chain BB [auth H] SDF format, chain EA [auth D] SDF format, chain FA [auth D] SDF format, chain L [auth B] SDF format, chain OA [auth F] SDF format, chain PA [auth F] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain BB [auth H] MOL2 format, chain EA [auth D] MOL2 format, chain FA [auth D] MOL2 format, chain L [auth B] MOL2 format, chain OA [auth F] MOL2 format, chain PA [auth F] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain BB [auth H] mmCIF format, chain EA [auth D] mmCIF format, chain FA [auth D] mmCIF format, chain L [auth B] mmCIF format, chain OA [auth F] mmCIF format, chain PA [auth F] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	BB [auth H] EA [auth D] FA [auth D] L [auth B] OA [auth F] BB [auth H], EA [auth D], FA [auth D], L [auth B], OA [auth F], PA [auth F], R [auth B], S [auth B]	MALONATE ION C₃ H₂ O₄ OFOBLEOULBTSOW-UHFFFAOYSA-L		Interactions Focus chain BB [auth H] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain L [auth B] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain BB [auth H] Focus chain EA [auth D] Focus chain FA [auth D] Focus chain L [auth B] Focus chain OA [auth F] Focus chain PA [auth F] Focus chain R [auth B] Focus chain S [auth B]
ACY Query on ACY Download:Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain AB [auth H] SDF format, chain DA [auth D] SDF format, chain M [auth B] SDF format, chain Q [auth B] MOL2 format, chain AA [auth D] MOL2 format, chain AB [auth H] MOL2 format, chain DA [auth D] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth B] mmCIF format, chain AA [auth D] mmCIF format, chain AB [auth H] mmCIF format, chain DA [auth D] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth B]	AA [auth D], AB [auth H], DA [auth D], M [auth B], Q [auth B]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain AB [auth H] Focus chain DA [auth D] Focus chain M [auth B] Focus chain Q [auth B] Interactions & Density Focus chain AA [auth D] Focus chain AB [auth H] Focus chain DA [auth D] Focus chain M [auth B] Focus chain Q [auth B]
FMT Query on FMT Download:Ideal Coordinates CCD File SDF format, chain P [auth B] MOL2 format, chain P [auth B] mmCIF format, chain P [auth B]	P [auth B]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain P [auth B] Interactions & Density Focus chain P [auth B]
CA Query on CA Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain F [auth B] SDF format, chain G [auth B] SDF format, chain HA [auth F] SDF format, chain IA [auth F] SDF format, chain QA [auth H] SDF format, chain RA [auth H] SDF format, chain SA [auth H] SDF format, chain T [auth D] SDF format, chain U [auth D] SDF format, chain V [auth D] SDF format, chain GA [auth F] MOL2 format, chain E [auth B] MOL2 format, chain F [auth B] MOL2 format, chain G [auth B] MOL2 format, chain HA [auth F] MOL2 format, chain IA [auth F] MOL2 format, chain QA [auth H] MOL2 format, chain RA [auth H] MOL2 format, chain SA [auth H] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D] MOL2 format, chain V [auth D] MOL2 format, chain GA [auth F] mmCIF format, chain E [auth B] mmCIF format, chain F [auth B] mmCIF format, chain G [auth B] mmCIF format, chain HA [auth F] mmCIF format, chain IA [auth F] mmCIF format, chain QA [auth H] mmCIF format, chain RA [auth H] mmCIF format, chain SA [auth H] mmCIF format, chain T [auth D] mmCIF format, chain U [auth D] mmCIF format, chain V [auth D] mmCIF format, chain GA [auth F]	E [auth B] F [auth B] G [auth B] GA [auth F] HA [auth F] E [auth B], F [auth B], G [auth B], GA [auth F], HA [auth F], IA [auth F], QA [auth H], RA [auth H], SA [auth H], T [auth D], U [auth D], V [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain SA [auth H] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D] Interactions & Density Focus chain E [auth B] Focus chain F [auth B] Focus chain G [auth B] Focus chain GA [auth F] Focus chain HA [auth F] Focus chain IA [auth F] Focus chain QA [auth H] Focus chain RA [auth H] Focus chain SA [auth H] Focus chain T [auth D] Focus chain U [auth D] Focus chain V [auth D]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain J [auth B] SDF format, chain K [auth B] SDF format, chain KA [auth F] SDF format, chain UA [auth H] SDF format, chain VA [auth H] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain LA [auth F] MOL2 format, chain J [auth B] MOL2 format, chain K [auth B] MOL2 format, chain KA [auth F] MOL2 format, chain UA [auth H] MOL2 format, chain VA [auth H] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain LA [auth F] mmCIF format, chain J [auth B] mmCIF format, chain K [auth B] mmCIF format, chain KA [auth F] mmCIF format, chain UA [auth H] mmCIF format, chain VA [auth H] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain LA [auth F]	J [auth B] K [auth B] KA [auth F] LA [auth F] UA [auth H] J [auth B], K [auth B], KA [auth F], LA [auth F], UA [auth H], VA [auth H], Y [auth D], Z [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain J [auth B] Focus chain K [auth B] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain UA [auth H] Focus chain VA [auth H] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain J [auth B] Focus chain K [auth B] Focus chain KA [auth F] Focus chain LA [auth F] Focus chain UA [auth H] Focus chain VA [auth H] Focus chain Y [auth D] Focus chain Z [auth D]