9RDI: Flap Endonuclease FEN1 with Compound 5

Crystal Structure of Flap Endonuclease FEN1 with Compound 5. Determined by X-ray diffraction at 2.1 Å resolution. Released 24 Sept 2025.

Method: X-ray diffraction
Resolution: 2.1 Å
Organism: Homo sapiens
Chains: 2
Atoms: 5,302
Mol. weight: 92.48 kDa
Ligands: A1JED, TEW, MG
Released: 24 Sept 2025

Explore 9RDI in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9RDI contains 43 α-helices and 14 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 22 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8
α-helix	15-17	3
β-strand	18-21	4	1
α-helix	23-26	4
β-strand	30-34	5	1
α-helix	35-44	10
α-helix	62-76	15
β-strand	80-85	6	1
α-helix	89-90	2
α-helix	101-113	13
α-helix	123-129	7
α-helix	135-148	14
β-strand	152-154	3	1
α-helix	159-168	10
β-strand	174-176	3	1
α-helix	181-184	4
β-strand	189-192	4	1
α-helix	203	1
β-strand	204-208	5	1
α-helix	209-216	8
α-helix	220-230	11
α-helix	243-253	11
α-helix	256-260	5
α-helix	269-271	3
α-helix	276-284	9
α-helix	291-293	3
α-helix	303-307	5
α-helix	308-313	6
α-helix	318-332	15

Chain B: 21 helices, 7 β-strands

Element	Residues	Length	Sheet
α-helix	6-13	8
α-helix	15-17	3
β-strand	18-21	4	2
β-strand	30-34	5	2
α-helix	35-44	10
α-helix	62-76	15
β-strand	80-85	6	2
α-helix	89-91	3
α-helix	101-113	13
α-helix	123-129	7
α-helix	135-148	14
β-strand	152-154	3	2
α-helix	159-168	10
β-strand	174-176	3	2
α-helix	181-184	4
β-strand	189-192	4	2
β-strand	204-208	5	2
α-helix	209-216	8
α-helix	220-230	11
α-helix	236-238	3
α-helix	243-253	11
α-helix	256-262	7
α-helix	269-271	3
α-helix	276-284	9
α-helix	299-301	3
α-helix	303-307	5
α-helix	308-313	6
α-helix	318-332	15

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Flap endonuclease 1	A, B	protein	342	Homo sapiens	P39748 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>9RDI_1 Flap endonuclease 1 (chains A, B)
MGIQGLAKLIADVAPSAIRENDIKSYFGRKVAIDASMSIYQFLIAVRQGGDVLQNEEGET
TSHLMGMFYRTIRMMENGIKPVYVFDGKPPQLKSGELAKRSERRAEAEKQLQQAQAAGAE
QEVEKFTKRLVKVTKQHNDECKHLLSLMGIPYLDAPSEAEASCAALVKAGKVYAAATEDM
DCLTFGSPVLMRHLTASEAKKLPIQEFHLSRILQELGLNQEQFVDLCILLGSDYCESIRG
IGPKRAVDLIQKHKSIEEIVRRLDPNKYPVPENWLHKEAHQLFLEPEVLDPESVELKWSE
PNEEELIKFMCGEKQFSEERIRSGVKRLSKSRQGSTLEVLFQ

Ligands and cofactors

ID	Name	Formula	Copies
A1JED	2-methyl-9-oxidanyl-6-(phenylmethyl)-3,4-dihydropyrazino[1,2-c]pyrimidine-1,8-d…	C15 H15 N3 O3	2
TEW	6-tungstotellurate(VI)	O24 Te W6	9
MG	Magnesium ion	Mg	4

Primary citation

Fragment-Based Discovery and Structure-Led Optimization of MSC778, the First Potent, Selective, and Orally Bioavailable FEN1 Inhibitor. Mann, S.E., Lefranc, J., Alkhatib, O. et al. J Med Chem (2025) 68:20410-20434. DOI 10.1021/acs.jmedchem.5c01526 · PubMed

Other PDB entries of the same protein (UniProt P39748 (AlphaFold model), which also has an AlphaFold model), best resolution first:

9RCI 1.66 Å, Crystal Structure of Flap Endonuclease FEN1 with Compound 28
1U7B 1.88 Å, Crystal structure of hPCNA bound to residues 331-350 of the flap endonuclease-1 (FEN1)
5ZOD 1.9 Å, Crystal Structure of hFen1 in apo form
5ZOE 1.95 Å, Crystal Structure of D181A hFen1 in complex with DNA
5E0V 2.07 Å, Human PCNA variant (S228I) complexed with FEN1 at 2.1 Angstroms
5K97 2.1 Å, Flap endonuclease 1 (FEN1) D233N with cleaved product fragment and Sm3+
5KSE 2.1 Å, Flap endonuclease 1 (FEN1) R100A with 5'-flap substrate DNA and Sm3+
3Q8K 2.2 Å, Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with product 5'-flap…
5ZOF 2.25 Å, Crystal Structure of D181A/R192F hFen1 in complex with DNA
5ZOG 2.3 Å, Crystal Structure of R192F hFen1 in complex with DNA
3Q8L 2.32 Å, Crystal Structure of Human Flap Endonuclease FEN1 (WT) in complex with substrate 5'-flap…
3UVU 2.38 Å, Structural basis of nuclear import of Flap endonuclease 1 (FEN1)

Browse structure collections

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