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- PDB-9gu8: NCS-1 bound to a FDA ligand 4 -

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Basic information

Entry
Database: PDB / ID: 9gu8
TitleNCS-1 bound to a FDA ligand 4
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
Chem-YG7 / Neuronal calcium sensor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsMunoz-Reyes, D. / Perez-Suarez, S. / 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 19, 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)21,81211
Polymers20,5431
Non-polymers1,26810
Water1,69394
1
B: Neuronal calcium sensor 1
hetero molecules

B: Neuronal calcium sensor 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,62322
Polymers41,0862
Non-polymers2,53720
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_555-x,y,-z+1/21
Buried area5220 Å2
ΔGint-147 kcal/mol
Surface area17320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)44.608, 102.912, 76.718
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Space group name HallC2c2
Symmetry operation#1: x,y,z
#2: x,-y,-z
#3: -x,y,-z+1/2
#4: -x,-y,z+1/2
#5: x+1/2,y+1/2,z
#6: x+1/2,-y+1/2,-z
#7: -x+1/2,y+1/2,-z+1/2
#8: -x+1/2,-y+1/2,z+1/2
Components on special symmetry positions
IDModelComponents
11B-376-

HOH

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Components

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Protein , 1 types, 1 molecules B

#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 BL21 (bacteria) / References: UniProt: P62166

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Non-polymers , 6 types, 104 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-YG7 / 5-{4-[4-(5-cyano-1H-indol-3-yl)butyl]piperazin-1-yl}-1-benzofuran-2-carboxamide


Mass: 441.525 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27N5O2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.14 Å3/Da / Density % sol: 42.6 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop
Details: 20% PEG 3000, 100 mM HEPES pH 7.5, 200 mM sodium acetate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALBA / Beamline: XALOC / Wavelength: 0.979 Å
DetectorType: DECTRIS PILATUS3 X 6M / Detector: PIXEL / Date: Jan 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.615→51.46 Å / Num. obs: 187441 / % possible obs: 89.3 % / Redundancy: 17.1 % / Biso Wilson estimate: 30.64 Å2 / CC1/2: 0.999 / Net I/σ(I): 17.1
Reflection shellResolution: 1.615→1.824 Å / Num. unique obs: 6794 / CC1/2: 0.465

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Processing

Software
NameVersionClassification
autoPROCdata reduction
Aimlessdata scaling
PHASERphasing
PHENIX1.21.1-5286refinement
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.67→51.46 Å / SU ML: 0.1602 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 36.2542
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.234 721 4.76 %
Rwork0.2055 14421 -
obs0.2069 15142 72.43 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 46.79 Å2
Refinement stepCycle: LAST / Resolution: 1.67→51.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1331 0 62 94 1487
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00451444
X-RAY DIFFRACTIONf_angle_d0.63751941
X-RAY DIFFRACTIONf_chiral_restr0.0385198
X-RAY DIFFRACTIONf_plane_restr0.0101250
X-RAY DIFFRACTIONf_dihedral_angle_d16.204553
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.80.3598220.3326505X-RAY DIFFRACTION12.83
1.8-1.980.2961000.29262137X-RAY DIFFRACTION54.27
1.98-2.270.25681880.22183690X-RAY DIFFRACTION93.33
2.27-2.860.2522100.22483957X-RAY DIFFRACTION99.83
2.86-51.460.21832010.18824132X-RAY DIFFRACTION99.86
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)
17.801758712475.12605870677-1.476126155976.298276350231.242971276879.34688510282-0.1909217899750.5349836969940.9640334728540.08804345570060.4660892250660.974904851601-0.885656917392-0.239192883664-0.1211959305550.3858359681070.155733431730.08890868705360.334304274820.04391197635740.485595992906-16.24139527292.845566235866.80079068083
22.37561220717-0.6294017455310.2284749994183.12617982210.3868557854562.50295090963-0.214344550618-0.3136240443480.1100566212130.919861113490.233416170753-0.03026155529040.02363964676580.2944162917630.01568020742340.419902606430.04974048741520.002166314948410.288674350619-0.08637498098560.221331505467-3.34090390894-5.5656502707113.4435084143
35.02233928018-1.22747600131-0.9667905551613.95806806452-0.02369275750052.55070044327-0.1418188046820.1007394607780.09630395507480.4440365133030.06412551444920.0356571186654-0.12099575818-0.1975737468560.01274971676990.18135145407-0.006068031936660.01324387736920.132255261011-0.01998178547610.114788516869-4.95936256754-12.26890978956.53872659433
44.922790576370.166907874884-0.4957228961174.320166964361.510953130264.25898499019-0.04645832631720.0912202352606-0.9243071825530.1543657847340.0242465313151-0.1737155221390.2776126744210.2060618060920.0202545075970.1667380359080.002097755194210.05965071199050.1363483087350.006738460785850.26437463085-3.58865720039-26.47883404155.91354386694
56.96611387867-1.13067682165-1.292865886265.303545899111.15670788995.77695028824-0.36586595102-0.165799055786-1.373670395080.6539969508590.1292538402590.05396570359760.78526453033-0.1921555479150.2216240220560.263685156834-0.02105365648580.05814896905110.227466227087-0.08357706128260.704522631569-8.87645079689-35.76081463114.98514299904
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 5 through 19)5 - 191 - 15
22chain 'B' and (resid 20 through 58 )20 - 5816 - 54
33chain 'B' and (resid 59 through 96 )59 - 9655 - 92
44chain 'B' and (resid 97 through 144 )97 - 14493 - 131
55chain 'B' and (resid 145 through 175 )145 - 175132 - 162

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