3ARA: Deoxyuridine 5'-triphosphate nucleotidohydrolase

Discovery of Novel Uracil Derivatives as Potent Human dUTPase Inhibitors. Determined by X-ray diffraction at 1.7 Å resolution. Released 8 Dec 2010.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,410
Mol. weight: 54.77 kDa
Ligands: MG, MKH
Released: 8 Dec 2010

Explore 3ARA in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3ARA contains 7 α-helices and 42 β-strands across 3 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: 3 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	1
β-strand	39	1	2
β-strand	47-51	5	2
β-strand	56-58	3	3
β-strand	62-67	6	4
β-strand	70-73	4	1
α-helix	74-75	2
β-strand	78-83	6	2
α-helix	86-92	7
β-strand	94-97	4	4
β-strand	100-101	2	2
β-strand	110-115	6	4
β-strand	121-123	3	3
α-helix	124	1
β-strand	128-136	9	2
β-strand	137-138	2	5
β-strand	141-144	4	6

Chain B: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	26-30	5	7
β-strand	39	1	8
β-strand	47-51	5	8
β-strand	56-58	3	9
β-strand	62-67	6	10
β-strand	70-73	4	7
α-helix	74-75	2
β-strand	78-83	6	8
α-helix	86-92	7
β-strand	94-97	4	10
β-strand	100-101	2	8
β-strand	110-115	6	10
β-strand	121-123	3	9
β-strand	128-136	9	8
β-strand	137	1	2
β-strand	141-144	4	1

Chain C: 2 helices, 14 β-strands

Element	Residues	Length	Sheet
β-strand	25-30	6	6
β-strand	39	1	5
β-strand	47-51	5	5
β-strand	56-58	3	11
β-strand	62-67	6	12
β-strand	70-73	4	6
α-helix	74-75	2
β-strand	78-83	6	5
α-helix	86-92	7
β-strand	94-97	4	12
β-strand	100-101	2	5
β-strand	110-115	6	12
β-strand	121-123	3	11
β-strand	128-136	9	5
β-strand	137-138	2	8
β-strand	142-144	3	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Deoxyuridine 5'-triphosphate nucleotidohydrolase	A, B, C	protein	164	Homo sapiens	P33316 (AlphaFold model)

Sequence of entity 1 (A, B, C), FASTA

>3ARA_1 Deoxyuridine 5'-triphosphate nucleotidohydrolase (chains A, B, C)
MPCSEETPAISPSKRARPAEVGGMQLRFARLSEHATAPTRGSARAAGYDLYSAYDYTIPP
MEKAVVKTDIQIALPSGCYGRVAPRSGLAAKHFIDVGAGVIDEDYRGNVGVVLFNFGKEK
FEVKKGDRIAQLICERIFYPEIEEVQALDDTERGSGGFGSTGKN

Ligands and cofactors

ID	Name	Formula	Copies
MG	Magnesium ion	Mg	2
MKH	1-[3-({(2R)-2-[hydroxy(diphenyl)methyl]pyrrolidin-1-yl}sulfonyl)propyl]pyrimidi…	C24 H27 N3 O5 S	3

Primary citation

Synthesis and discovery of N-carbonylpyrrolidine- or N-sulfonylpyrrolidine-containing uracil derivatives as potent human deoxyuridine triphosphatase inhibitors. Miyakoshi, H., Miyahara, S., Yokogawa, T. et al. J Med Chem (2012) 55:2960-2969. DOI 10.1021/jm201627n · PubMed

Other PDB entries of the same protein (UniProt P33316 (AlphaFold model), which also has an AlphaFold model), best resolution first:

3ARN 1.8 Å, Human dUTPase in complex with novel uracil derivative
3EHW 1.8 Å, Human dUTPase in complex with alpha,beta-imido-dUTP and Mg2+: visualization of the…
5H4J 1.8 Å, Crystal structure of Human dUTPase in complex with N-[(1R)-1-[3-(Cyclopentyloxy)-phenyl]-…
4MZ6 1.88 Å, Structure of importin-alpha: dUTPase S11E NLS mutant complex
7PWJ 1.94 Å, dUTPase from human in complex with Stl
1Q5H 2.0 Å, Human dUTP Pyrophosphatase complex with dUDP
1Q5U 2.0 Å, Human dutp pyrophosphatase
24OK 2.01 Å, Crystal structure of human dUTPase complexed with Zinc.
4MZ5 2.1 Å, Structure of importin-alpha: dUTPase NLS complex
2HQU 2.2 Å, Human dUTPase in complex with alpha,beta-iminodUTP and magnesium ion
8C8I 3.2 Å, Human dUTPase in complex with a potent proteinaceous inhibitor (Stl)

Browse structure collections

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