Protein profile

PA0441

D-hydantoinase/dihydropyrimidinase

Genome: NC_002516.2

Gene: PA0441 dht Structure source: Experimental + AlphaFold UniProt Q9I676
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Amino acids 479
Annotations 10
Features 15
PDB binders 7
Druggability 0.707

Overview

Basic information about this protein and its source genome.

Accession
PA0441
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA0441 dht
Status
annotated
Amino acids
479
Structure source
Experimental + AlphaFold
EC
3.5.2.2
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0004157 Catalysis of the reaction: 5,6-dihydrouracil + H2O = 3-ureidopropionate. GO:0016812 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide. GO:0046872 Binding to a metal ion. GO:0055086 The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide. GO:0072527 The chemical reactions and pathways involving a pyrimidine-containing compound, i.e. any compound that contains pyrimidine or a formal derivative thereof.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
51.24
Human E-value
1.3e-170
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.707
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0004157 Catalysis of the reaction: 5,6-dihydrouracil + H2O = 3-ureidopropionate.
  • GO:0016812 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide.
  • GO:0046872 Binding to a metal ion.
  • GO:0055086 The cellular chemical reactions and pathways involving a nucleobase-containing small molecule: a nucleobase, a nucleoside, or a nucleotide.
  • GO:0072527 The chemical reactions and pathways involving a pyrimidine-containing compound, i.e. any compound that contains pyrimidine or a formal derivative thereof.
  • GO:0016810 Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
3 450 CDD cd01314 D-HYD
3 450 InterPro IPR011778 Hydantoinase/dihydropyrimidinase
50 436 Pfam PF01979 Amidohydrolase family
50 436 InterPro IPR006680 Amidohydrolase-related
54 383 SUPERFAMILY SSF51556 Metallo-dependent hydrolases
54 383 InterPro IPR032466 Metal-dependent hydrolase
54 424 FunFam G3DSA:3.20.20.140:FF:000001 Dihydropyrimidinase like 3
54 424 Gene3D G3DSA:3.20.20.140 -
3 455 NCBIfam TIGR02033 dihydropyrimidinase
3 455 InterPro IPR011778 Hydantoinase/dihydropyrimidinase
2 470 PANTHER PTHR11647 HYDRANTOINASE/DIHYDROPYRIMIDINASE FAMILY MEMBER
1 455 SUPERFAMILY SSF51338 Composite domain of metallo-dependent hydrolases
1 455 InterPro IPR011059 Metal-dependent hydrolase, composite domain superfamily
2 465 Gene3D G3DSA:2.30.40.10 Urease, subunit C, domain 1
2 465 InterPro IPR011059 Metal-dependent hydrolase, composite domain superfamily

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

6 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 6KLK
X-ray 1.76 Å A,B
100.0% 1-479
PDBe RCSB PDBj File
Viewing
PDB 8WQ9
X-ray 1.97 Å A,B
100.0% 1-479
PDBe RCSB PDBj File
Loaded
PDB 5E5C
X-ray 2.10 Å A,C
100.0% 1-479
PDBe RCSB PDBj File
Loaded
PDB 7E3U
X-ray 2.16 Å A,B
100.0% 1-479
PDBe RCSB PDBj File
Loaded
PDB 5YKD
X-ray 2.17 Å A,B,C,D
100.0% 1-479
PDBe RCSB PDBj File
Loaded
PDB 6AJD
X-ray 2.22 Å A,B
100.0% 1-479
PDBe RCSB PDBj File
Loaded
AlphaFold PA0441
AlphaFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
3 0.295
5 0.236

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 5.27 0.246
2 4.66 0.203
3 4.36 0.182
4 3.02 0.099
5 2.62 0.076

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

63 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
URF
6KLK 1.76 Å Open crystal
130.1 Da LogP -0.80 TPSA 65.7 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1)F

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.