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- PDB-9ifu: FSP1 (tetrapod ancestor) bound to FAD and NAD+ and compound 1 -

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Basic information

Entry
Database: PDB / ID: 9ifu
TitleFSP1 (tetrapod ancestor) bound to FAD and NAD+ and compound 1
ComponentsFSP1 (tetrapod ancestor)
KeywordsOXIDOREDUCTASE / Flavin / NAD / coenzyme Q / ferroptosis / myristoylation / inhibitor discovery
Function / homology: / FLAVIN-ADENINE DINUCLEOTIDE / NICOTINAMIDE-ADENINE-DINUCLEOTIDE
Function and homology information
Biological speciesMammalia (mammals)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsCecchini, D. / Mattevi, A.
Funding supportEuropean Union, Italy, 2items
OrganizationGrant numberCountry
European Research Council (ERC)101094471European Union
Italian Association for Cancer Research28754 Italy
CitationJournal: To Be Published
Title: Best-in-Class FSP1 Inhibitors Unraveled By AI-Enhanced Adaptive Screening Platform
Authors: Cecchini, D. / Mattevi, A.
History
DepositionFeb 18, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 4, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: FSP1 (tetrapod ancestor)
B: FSP1 (tetrapod ancestor)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,41210
Polymers79,6212
Non-polymers3,7918
Water10,016556
1
A: FSP1 (tetrapod ancestor)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7115
Polymers39,8111
Non-polymers1,9014
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: FSP1 (tetrapod ancestor)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,7005
Polymers39,8111
Non-polymers1,8904
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)43.567, 79.684, 113.062
Angle α, β, γ (deg.)90.00, 98.61, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein FSP1 (tetrapod ancestor)


Mass: 39810.551 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mammalia (mammals) / Production host: Escherichia coli BL21 (bacteria)

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Non-polymers , 6 types, 564 molecules

#2: Chemical ChemComp-FAD / FLAVIN-ADENINE DINUCLEOTIDE


Mass: 785.550 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C27H33N9O15P2 / Comment: FAD*YM
#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-A1I3Y / (1,1-dimethyl-3,4-dihydroisochromen-6-yl)-[4-(3-phenyl-1~{H}-1,2,4-triazol-5-yl)piperidin-1-yl]methanone


Mass: 416.515 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H28N4O2 / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 556 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.06 M MgCl2, CaCl2, 0.1M imidazole/MES monohydrate (acid) pH 6.5, 12.5% MPD, 12.5% PEG1000, 12.5% PEG3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 9, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.55→64.97 Å / Num. obs: 46979 / % possible obs: 83.7 % / Redundancy: 2.5 % / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.079 / Rrim(I) all: 0.133 / Net I/σ(I): 5.1
Reflection shellResolution: 1.551→1.842 Å / % possible obs: 5.3 % / Redundancy: 2.6 % / Rmerge(I) obs: 0.393 / Num. measured all: 6050 / Num. unique obs: 2349 / Rpim(I) all: 0.279 / Rrim(I) all: 0.484 / Net I/σ(I) obs: 2.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0405refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→64.97 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.895 / SU B: 2.245 / SU ML: 0.085 / Cross valid method: THROUGHOUT / ESU R: 0.219 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24249 2279 4.9 %RANDOM
Rwork0.17919 ---
obs0.18222 44700 42.51 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 19.923 Å2
Baniso -1Baniso -2Baniso -3
1-0.08 Å20 Å2-0.14 Å2
2--0.06 Å2-0 Å2
3----0.09 Å2
Refinement stepCycle: 1 / Resolution: 1.55→64.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5544 0 258 556 6358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0126000
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165685
X-RAY DIFFRACTIONr_angle_refined_deg1.3411.6458162
X-RAY DIFFRACTIONr_angle_other_deg0.4391.57813135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.9955748
X-RAY DIFFRACTIONr_dihedral_angle_2_deg16.378522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.12101017
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.060.2922
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026834
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021262
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.7271.9232968
X-RAY DIFFRACTIONr_mcbond_other1.7261.9232968
X-RAY DIFFRACTIONr_mcangle_it2.7853.4453724
X-RAY DIFFRACTIONr_mcangle_other2.7853.4463725
X-RAY DIFFRACTIONr_scbond_it2.5672.3213032
X-RAY DIFFRACTIONr_scbond_other2.5672.3233033
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other4.314.1114439
X-RAY DIFFRACTIONr_long_range_B_refined6.43821.556947
X-RAY DIFFRACTIONr_long_range_B_other6.38721.076821
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.551→1.591 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.225 4 -
Rwork0.179 107 -
obs--1.37 %

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