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- PDB-9gto: NCS-1 bound to a FDA ligand 1 -

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Basic information

Entry
Database: PDB / ID: 9gto
TitleNCS-1 bound to a FDA ligand 1
ComponentsNeuronal calcium sensor 1
KeywordsMETAL BINDING PROTEIN / Neuronal calcium sensor 1 / EF-hand containing protein / drug repurposing / FDA ligand
Function / homology
Function and homology information


calcium sensitive guanylate cyclase activator activity / regulation of neuron projection development / regulation of signal transduction / voltage-gated calcium channel activity / postsynaptic density / axon / intracellular membrane-bounded organelle / calcium ion binding / dendrite / perinuclear region of cytoplasm ...calcium sensitive guanylate cyclase activator activity / regulation of neuron projection development / regulation of signal transduction / voltage-gated calcium channel activity / postsynaptic density / axon / intracellular membrane-bounded organelle / calcium ion binding / dendrite / perinuclear region of cytoplasm / Golgi apparatus / plasma membrane / cytoplasm / cytosol
Similarity search - Function
Recoverin family / EF hand domain / EF-hand domain pair / EF-hand, calcium binding motif / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
: / Neuronal calcium sensor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsMunoz-Reyes, D. / Miro-Rodriguez, C. / Sanchez-Barrena, M.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Ministerio de Ciencia e Innovacion (MCIN)PID2022-137331OB-C31 Spain
CitationJournal: J.Med.Chem. / Year: 2025
Title: FDA Drug Repurposing Uncovers Modulators of Dopamine D 2 Receptor Localization via Disruption of the NCS-1 Interaction.
Authors: 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, ...Authors: 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.
History
DepositionSep 18, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 19, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
B: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,3887
Polymers20,5431
Non-polymers8456
Water1,35175
1
B: Neuronal calcium sensor 1
hetero molecules

B: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,77614
Polymers41,0862
Non-polymers1,69012
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area6510 Å2
ΔGint-108 kcal/mol
Surface area19390 Å2
MethodPISA
Unit cell
Length a, b, c (Å)111.110, 34.501, 55.338
Angle α, β, γ (deg.)90.000, 95.860, 90.000
Int Tables number5
Space group name H-MC121
Space group name HallC2y
Symmetry operation#1: x,y,z
#2: -x,y,-z
#3: x+1/2,y+1/2,z
#4: -x+1/2,y+1/2,-z
Components on special symmetry positions
IDModelComponents
11B-370-

HOH

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Components

#1: Protein Neuronal calcium sensor 1 / NCS-1 / Frequenin homolog / Frequenin-like protein / Frequenin-like ubiquitous protein


Mass: 20543.092 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NCS1, FLUP, FREQ / Production host: Escherichia coli (E. coli) / References: UniProt: P62166
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-A1IPH / (5-methyl-2-oxidanylidene-1,3-dioxol-4-yl)methyl 2-ethoxy-3-[[4-[2-(5-oxidanylidene-4~{H}-1,2,4-oxadiazol-3-yl)phenyl]phenyl]methyl]benzimidazole-4-carboxylate


Mass: 568.534 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H24N4O8 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 75 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.57 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 70 % MPD, 100 mM HEPES pH 7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 Å
DetectorType: DECTRIS EIGER2 XE 9M / Detector: PIXEL / Date: May 6, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.873 Å / Relative weight: 1
ReflectionResolution: 2.141→55.265 Å / Num. obs: 25602 / % possible obs: 85.9 % / Redundancy: 4.7 % / Biso Wilson estimate: 36.32 Å2 / Rmerge(I) obs: 0.198 / Net I/σ(I): 4.7
Reflection shellResolution: 2.141→2.355 Å / Rmerge(I) obs: 1.751 / Num. unique obs: 1388

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Processing

Software
NameVersionClassification
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.21.1-5286refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.3→37.15 Å / SU ML: 0.2815 / Cross valid method: FREE R-VALUE / σ(F): 1.92 / Phase error: 29.1011
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2444 816 5.37 %
Rwork0.2127 14372 -
obs0.2145 15188 83.66 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 50.19 Å2
Refinement stepCycle: LAST / Resolution: 2.3→37.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1385 0 53 75 1513
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00251468
X-RAY DIFFRACTIONf_angle_d0.45831977
X-RAY DIFFRACTIONf_chiral_restr0.0361199
X-RAY DIFFRACTIONf_plane_restr0.004257
X-RAY DIFFRACTIONf_dihedral_angle_d15.0088545
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.3-2.440.3067760.2981318X-RAY DIFFRACTION45.96
2.44-2.630.30131430.27052268X-RAY DIFFRACTION79.44
2.63-2.90.30291670.27432592X-RAY DIFFRACTION91.45
2.9-3.320.26821550.22952703X-RAY DIFFRACTION95.01
3.32-4.180.23181430.17882766X-RAY DIFFRACTION96.17
4.18-37.150.1991320.18942725X-RAY DIFFRACTION94.14
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.000802468496.742846927813.049487423578.53696859757-2.602004503542.004177533440.328640012374-0.974561226262-1.091090890231.57916223716-0.145774648253-2.209294895440.2715883219991.43470692037-0.1783847554570.6059412192430.131692643938-0.1337226767030.760909481429-0.06568500415040.78670450967643.9763342727-13.400786506718.5768122122
20.788699622397-1.196284120530.2793247813842.763568317860.1801843988290.497269808180.0190146286890.1750732852150.174185158779-0.0278390080506-0.0382539389807-0.08518409-0.1175974239030.2634510511130.02457479817270.399873420707-0.09696478786840.0681910390670.388134062299-0.02418289035670.37863903642134.0253196466-1.205068408779.08376984024
32.86827405154-0.246678433197-0.06163157429231.71849856972-0.6033583034222.18929338862-0.07254925535820.00558517062074-0.3181269753730.07869110758110.1051756898950.1151605568950.01611592013140.225254441159-0.03343139923650.235116777217-0.0175351713647-0.004447447885470.204126947849-0.0545560956750.30032239740727.5969516667-3.1919200843516.5093931042
42.47513190572-1.749442247591.529162243763.17288109076-3.107490598516.0814414023-0.0660057686048-0.00173386781738-0.1302784093690.07065681738370.1422818483340.302668172855-0.10666809731-0.534056081828-0.04227905199460.192134966417-0.0357720740384-0.001231283724580.2623933185950.004729418826030.34113803520712.7108345494-4.5931248818813.2855642812
58.711271736030.8782006633683.658294927854.141641534493.704765139776.537027395720.161352469550.091707386811-0.9150119074890.1211049561230.312780540942-0.5534971418450.4481496088530.779341412288-0.4606845598890.2859147210670.060796666695-0.02564528210970.356651389369-0.02299633871940.406179232747-5.84269439702-12.4050025448-19.0740289383
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: B / Label asym-ID: D

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'B' and (resid 9 through 19 )9 - 193 - 13
22chain 'B' and (resid 20 through 58 )20 - 5814 - 52
33chain 'B' and (resid 59 through 96 )59 - 9653 - 90
44chain 'B' and (resid 97 through 144 )97 - 14491 - 138
55chain 'B' and (resid 145 through 174 )145 - 174139 - 168

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