Protein profile

PA4172

nuclease

Genome: NC_002516.2

Gene: PA4172 Structure source: AlphaFold UniProt Q9HWK9
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Amino acids 266
Annotations 9
Features 17
PDB binders 1
Druggability 0.665

Overview

Basic information about this protein and its source genome.

Accession
PA4172
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA4172
Status
annotated
Amino acids
266
Structure source
AlphaFold
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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). GO:0008311 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA molecule. GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks. GO:0046872 Binding to a metal ion. GO:0006974 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
45.652
Human E-value
6.32e-06
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 0.665
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MDTLKIATFNVNGIQTRLAALLAWLEREAPDIVCLQELKTPDARFPAAALEKAGYGAIWQGQSAWNGVAILARDSQPLEVRRGLPGNASDPHSRYLEAAVDGLLVASLYLPNGNPQPGPKFDYKLAWFEHLIRHAAELMESGHPVVLAGDFNVVPSDFDIYDTRSWKKDALLQPESRECFERLLRQGWVDALRQRFPDRRLYTFWDYFRQHWQRDAGLRIDHLLLSASLADHLEDAGVDRWVRGEEHASDHAPAWVSLRRPSEPRR

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0008311 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of a double-stranded DNA molecule.
  • GO:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks.
  • GO:0046872 Binding to a metal ion.
  • GO:0006974 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0004518 Catalysis of the cleavage of ester linkages within nucleic acids.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
4 260 ProSiteProfiles PS51435 AP endonucleases family 1 profile.
4 260 InterPro IPR004808 AP endonuclease 1
30 39 ProSitePatterns PS00726 AP endonucleases family 1 signature 1.
30 39 InterPro IPR020847 AP endonuclease 1, binding site
4 257 NCBIfam TIGR00195 exodeoxyribonuclease III
4 258 SUPERFAMILY SSF56219 DNase I-like
4 258 InterPro IPR036691 Endonuclease/exonuclease/phosphatase superfamily
1 260 PANTHER PTHR43250 -
1 260 InterPro IPR037493 Exodeoxyribonuclease III-like
7 251 Pfam PF03372 Endonuclease/Exonuclease/phosphatase family
7 251 InterPro IPR005135 Endonuclease/exonuclease/phosphatase
4 258 NCBIfam TIGR00633 exodeoxyribonuclease III
4 258 InterPro IPR004808 AP endonuclease 1
4 258 CDD cd09086 ExoIII-like_AP-endo
4 258 InterPro IPR037493 Exodeoxyribonuclease III-like
4 259 Gene3D G3DSA:3.60.10.10 Endonuclease/exonuclease/phosphatase
4 259 InterPro IPR036691 Endonuclease/exonuclease/phosphatase superfamily

3D Structure

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

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Structural evidence

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA4172
AlphaFold — — full sequence — Viewing
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
1 0.665

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.

151 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
PGA
5WN2
P27695 156.0 Da LogP -0.82 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)O)OP(=O)(O)O

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.