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- PDB-9t0h: NCS-1 bound to a FDA-approved drug -

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Basic information

Entry
Database: PDB / ID: 9t0h
TitleNCS-1 bound to a FDA-approved drug
ComponentsNeuronal calcium sensor 1
KeywordsMETAL BINDING PROTEIN / Complex / modulator
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 / intracellular membrane-bounded organelle / postsynaptic density / axon / 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 / intracellular membrane-bounded organelle / postsynaptic density / axon / 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
ETHANOL / Chem-H9F / DI(HYDROXYETHYL)ETHER / Neuronal calcium sensor 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.91 Å
AuthorsMiro-Rodriguez, C. / Sanchez-Barrena, M.J.
Funding support Spain, 1items
OrganizationGrant numberCountry
Spanish Ministry of Science, Innovation, and UniversitiesPID2022-137331OB-C31 Spain
CitationJournal: Eur.J.Med.Chem. / Year: 2026
Title: An AI-based approach accelerates the discovery of protein-protein interaction modulators targeting NCS-1.
Authors: 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.
History
DepositionOct 17, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 11, 2026Provider: repository / Type: Initial release
Revision 1.1Mar 18, 2026Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title

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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)21,00711
Polymers19,8551
Non-polymers1,15110
Water2,684149
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1810 Å2
ΔGint-54 kcal/mol
Surface area10110 Å2
Unit cell
Length a, b, c (Å)45.327, 103.021, 76.294
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-404-

HOH

21B-441-

HOH

31B-449-

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: 19855.303 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 , 7 types, 159 molecules

#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-P6G / HEXAETHYLENE GLYCOL / POLYETHYLENE GLYCOL PEG400


Mass: 282.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C12H26O7 / Comment: precipitant*YM
#5: Chemical ChemComp-H9F / 2-[[2-[bis(2-hydroxyethyl)amino]-4,8-di(piperidin-1-yl)pyrimido[5,4-d]pyrimidin-6-yl]-(2-hydroxyethyl)amino]ethanol


Mass: 504.626 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H40N8O4 / Feature type: SUBJECT OF INVESTIGATION / Comment: inhibitor*YM
#6: Chemical ChemComp-EOH / ETHANOL


Mass: 46.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O
#7: Chemical ChemComp-NA / SODIUM ION


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


Mass: 18.015 Da / Num. of mol.: 149 / 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: 2.17 Å3/Da / Density % sol: 43.41 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES pH 7.5, 25% PEG 2000 MME

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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: Sep 21, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.748→51.511 Å / Num. obs: 12143 / % possible obs: 87.6 % / Redundancy: 12.8 % / Biso Wilson estimate: 32.68 Å2 / CC1/2: 0.992 / Net I/σ(I): 10.1
Reflection shellResolution: 1.748→1.967 Å / Num. unique obs: 607 / CC1/2: 0.587

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Processing

Software
NameVersionClassification
PHENIX1.21.2_5419refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.91→38.15 Å / SU ML: 0.2381 / Cross valid method: FREE R-VALUE / σ(F): 1.38 / Phase error: 32.0556
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2545 580 4.9 %
Rwork0.2104 11251 -
obs0.2127 11831 83.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 52.42 Å2
Refinement stepCycle: LAST / Resolution: 1.91→38.15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1369 0 73 149 1591
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0041508
X-RAY DIFFRACTIONf_angle_d0.67862023
X-RAY DIFFRACTIONf_chiral_restr0.0377204
X-RAY DIFFRACTIONf_plane_restr0.0069267
X-RAY DIFFRACTIONf_dihedral_angle_d14.5386614
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.91-2.10.3061600.27491333X-RAY DIFFRACTION39.96
2.1-2.410.29471580.23333218X-RAY DIFFRACTION96.1
2.41-3.030.28011950.24393281X-RAY DIFFRACTION97.7
3.03-38.150.23151670.18843419X-RAY DIFFRACTION97.45
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)
15.25910229178-1.96752848661-1.575601668035.100517527620.8867444888252.6842745007-0.141184615638-0.1397341016460.811678334331.038110687670.339143857394-0.379205043879-0.4761260851470.142109625873-0.264117449250.5546906944820.04066815895880.01900124994340.290009021245-0.1110243114040.307048204997-8.08666753878-2.3176861544811.0914078925
23.13720273446-0.707807925659-1.332886854683.46817495102-0.001178026244083.692722762550.0597518459680.05585712821990.1132817391190.487969496330.0449599140233-0.0352839464567-0.3453859556920.0615797224976-0.07187381316490.1680306267-0.0108756558108-0.007077484435120.122996491608-0.0251698798250.132191943901-3.27807629212-12.55088033747.60285933664
36.97022654904-2.24119177331-0.2554619196137.037153032471.505604027272.865706316360.4327809411460.675296316618-0.233223079179-0.557043441114-0.390201847458-0.0619698609482-0.108131346857-0.1833841015670.1599392555580.1880571156080.01931828641960.04502427987880.22815631595-0.0126458034250.175140557425-9.80599834617-23.45004854383.35737146686
48.40386612179-0.08663994328270.8569727224817.807180802733.084999266687.18957918942-0.0380668842497-0.101941597695-0.7869496672940.439127424149-0.143664423767-0.7545114343470.405893622971-0.06626712212680.02824808877450.3026674195870.009284045606630.05719259608360.2007716638960.07565031769060.3016081244632.64928572333-28.8964030288.55793787097
52.99362359998-2.739684579191.668390546823.59076990394-0.8986224737992.22300850137-1.278603915750.200646543060.689869432705-3.211880210041.382047307621.84301323970.348407109678-0.41129383713-0.6682667658561.62925221604-0.1787556941210.04957369679621.03205463010.4085244152360.9005026217926.33044550867-36.747208790318.9060211626
68.13240701391-0.0456896598641.368294210335.21406178740.9231070070797.11821965774-0.4067584745080.00718719195539-1.343211535370.529615251207-0.3198174030580.3421019928471.41415024678-0.4240766585230.1997068574990.358413904915-0.05038287863840.06297817774430.22668402308-0.1478385889680.480477508242-9.22996756303-35.50380462424.74680566731
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 55 )5 - 551 - 51
22chain 'B' and (resid 56 through 94 )56 - 9452 - 90
33chain 'B' and (resid 95 through 117 )95 - 11791 - 113
44chain 'B' and (resid 118 through 132 )118 - 132114 - 128
55chain 'B' and (resid 133 through 144 )133 - 144129 - 136
66chain 'B' and (resid 145 through 174 )145 - 174137 - 166

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