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- PDB-9rdi: Crystal Structure of Flap Endonuclease FEN1 with Compound 5 -

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Basic information

Entry
Database: PDB / ID: 9rdi
TitleCrystal Structure of Flap Endonuclease FEN1 with Compound 5
ComponentsFlap endonuclease 1
KeywordsHYDROLASE / Endonuclease
Function / homology
Function and homology information


flap endonuclease activity / telomere maintenance via semi-conservative replication / positive regulation of sister chromatid cohesion / double-stranded DNA exodeoxyribonuclease activity / 5'-flap endonuclease activity / UV protection / DNA replication, removal of RNA primer / Removal of the Flap Intermediate / HDR through MMEJ (alt-NHEJ) / Removal of the Flap Intermediate from the C-strand ...flap endonuclease activity / telomere maintenance via semi-conservative replication / positive regulation of sister chromatid cohesion / double-stranded DNA exodeoxyribonuclease activity / 5'-flap endonuclease activity / UV protection / DNA replication, removal of RNA primer / Removal of the Flap Intermediate / HDR through MMEJ (alt-NHEJ) / Removal of the Flap Intermediate from the C-strand / 5'-3' exonuclease activity / exonuclease activity / Early Phase of HIV Life Cycle / POLB-Dependent Long Patch Base Excision Repair / PCNA-Dependent Long Patch Base Excision Repair / base-excision repair, gap-filling / double-strand break repair via homologous recombination / memory / RNA-DNA hybrid ribonuclease activity / double-strand break repair / manganese ion binding / double-stranded DNA binding / endonuclease activity / damaged DNA binding / Hydrolases; Acting on ester bonds / chromosome, telomeric region / DNA replication / DNA repair / nucleolus / magnesium ion binding / protein-containing complex / mitochondrion / DNA binding / nucleoplasm / nucleus / membrane
Similarity search - Function
Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region ...Flap endonuclease 1 / XPG protein signature 2. / XPG conserved site / XPG protein signature 1. / XPG/Rad2 endonuclease / XPG, N-terminal / XPG-I domain / XPG N-terminal domain / XPG I-region / Xeroderma pigmentosum G I-region / Xeroderma pigmentosum G N-region / Helix-hairpin-helix motif, class 2 / Helix-hairpin-helix class 2 (Pol1 family) motifs / 5'-3' exonuclease, C-terminal domain superfamily / PIN-like domain superfamily
Similarity search - Domain/homology
: / 6-tungstotellurate(VI) / Flap endonuclease 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.105 Å
AuthorsToste Rego, A. / Pica, A. / Cornaciu, I. / Burgdorf, L. / Mann, S.E.
Funding support United Kingdom, Germany, 2items
OrganizationGrant numberCountry
Other private United Kingdom
Other private Germany
CitationJournal: J.Med.Chem. / Year: 2025
Title: Fragment-Based Discovery and Structure-Led Optimization of MSC778, the First Potent, Selective, and Orally Bioavailable FEN1 Inhibitor.
Authors: Mann, S.E. / Lefranc, J. / Alkhatib, O. / Boivin, R. / Bomke, J. / Byrne, R.T. / Cassona, C.P. / Chen, X. / Cornaciu, I. / Costales, P. / Davis, O.A. / DeSelm, L. / Elinati, E. / Follows, B. ...Authors: Mann, S.E. / Lefranc, J. / Alkhatib, O. / Boivin, R. / Bomke, J. / Byrne, R.T. / Cassona, C.P. / Chen, X. / Cornaciu, I. / Costales, P. / Davis, O.A. / DeSelm, L. / Elinati, E. / Follows, B. / Galbiati, A. / Goldner, C. / Hayre, J.K. / Jorand-Lebrun, C. / Lademann, C.A. / Leuthner, B. / Majithiya, J.B. / Malta, C.F. / Mason, B. / McWhirter, C.L. / Neff, B. / Nissink, J.W.M. / Pehl, U. / Petersson, C. / Pica, A. / Pinto, M.F. / Rajendra, E. / Rakers, C. / Toste Rego, A. / Robinson, H.M.R. / Sala-Hojman, A. / Schaedler, T.A. / Schurmann, P.J.L. / Silva, D.O. / Smith, G.C.M. / Sorrell, F. / Webster, G.R. / Zenke, F.T. / Heald, R.A. / Burgdorf, L.T.
History
DepositionJun 2, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 24, 2025Provider: repository / Type: Initial release
Revision 1.1Oct 1, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 22, 2025Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Flap endonuclease 1
B: Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)92,48417
Polymers77,2852
Non-polymers15,19915
Water95553
1
A: Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,4358
Polymers38,6421
Non-polymers6,7927
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Flap endonuclease 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0499
Polymers38,6421
Non-polymers8,4078
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.453, 116.150, 139.706
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Flap endonuclease 1 / FEN-1 / DNase IV / Flap structure-specific endonuclease 1 / Maturation factor 1 / MF1 / hFEN-1


Mass: 38642.383 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FEN1, RAD2 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 RIL
References: UniProt: P39748, Hydrolases; Acting on ester bonds
#2: Chemical ChemComp-A1JED / 2-methyl-9-oxidanyl-6-(phenylmethyl)-3,4-dihydropyrazino[1,2-c]pyrimidine-1,8-dione


Mass: 285.298 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H15N3O3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-TEW / 6-tungstotellurate(VI)


Mass: 1614.626 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: O24TeW6
#4: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 53 / 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: 3.52 Å3/Da / Density % sol: 65.08 %
Crystal growTemperature: 277 K / Method: vapor diffusion
Details: 21 % PEG MME 5000, 0.1 M MES pH 6.5, 10 mM ammonium sulphate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 2 / Wavelength: 0.98011 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Oct 4, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98011 Å / Relative weight: 1
ReflectionResolution: 2.105→58.075 Å / Num. obs: 39509 / % possible obs: 67.2 % / Redundancy: 6.8 % / Biso Wilson estimate: 24.65 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.179 / Rpim(I) all: 0.076 / Rrim(I) all: 0.195 / Net I/σ(I): 8.2
Reflection shellResolution: 2.105→2.326 Å / Num. unique obs: 1975 / CC1/2: 0.502

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Processing

Software
NameVersionClassification
BUSTER2.11.8 (10-JUL-2024)refinement
PDB_EXTRACTdata extraction
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.105→40.41 Å / Cor.coef. Fo:Fc: 0.912 / Cor.coef. Fo:Fc free: 0.905 / SU R Cruickshank DPI: 0.272 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.265 / SU Rfree Blow DPI: 0.199 / SU Rfree Cruickshank DPI: 0.202
Details: HYDROGENS WERE FULLY REFINED WITH ZERO OCCUPANCY AT NUCLEAR POSITION.
RfactorNum. reflection% reflectionSelection details
Rfree0.2319 1963 4.97 %RANDOM
Rwork0.2113 ---
obs0.2123 39503 67.2 %-
Displacement parametersBiso mean: 38.62 Å2
Baniso -1Baniso -2Baniso -3
1-1.4913 Å20 Å20 Å2
2--6.1386 Å20 Å2
3----7.6299 Å2
Refine analyzeLuzzati coordinate error obs: 0.3 Å
Refinement stepCycle: LAST / Resolution: 2.105→40.41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4893 0 325 53 5271
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0095474HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.218122HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1824SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes873HARMONIC5
X-RAY DIFFRACTIONt_it5024HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.86
X-RAY DIFFRACTIONt_other_torsion17.49
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion646SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies1HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact3661SEMIHARMONIC4
LS refinement shellResolution: 2.105→2.25 Å
RfactorNum. reflection% reflection
Rfree0.2842 -4.05 %
Rwork0.2792 759 -
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)
11.9087-0.69650.51180.8225-0.37571.02780.01010.2114-0.05840.3958-0.03660.0306-0.10650.00780.02650.1036-0.02970.012-0.07290.0047-0.2188-18.644321.194-17.8861
20.72371.03970.60831.46190.52672.26510.1274-0.02880.0730.0043-0.06690.07360.10450.0527-0.0605-0.10710.01620.0281-0.0076-0.0409-0.0847-30.247720.5757-57.8898
30-0.60740.31070.31350.02311.71660.03860.0954-0.18230.1117-0.1038-0.15140.34870.09980.0651-0.0003-0.0115-0.00390.1233-0.0608-0.1435-25.068713.6757-44.4721
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1{ A|* }
2X-RAY DIFFRACTION2{ B|* }
3X-RAY DIFFRACTION3{ E|* }

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