Protein target profile

PA2386

L-ornithine N5-oxygenase

Genome: NC_002516.2

Gene: pvdA pvd-1 PA2386 3D evidence: Experimental + AlphaFold DB model UniProt Q51548
Export view
Length 443
Pocket druggability 0.725
Ligand records 53
EC / GO 1 / 5
Target summary

Promising target candidate with multiple supporting evidence streams.

6 signals

Strengths

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Strong predicted binding pocket FPocket selected-pocket score 0.72. This is a computational pocket signal, not binding validation. Structure available Experimental + AlphaFold DB model Direct ligand evidence 2 direct ligand records.

Risks / watch

No major risk signal surfaced in the loaded evidence.

Missing evidence

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
How to read this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal TPW pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Overview

Basic information about this protein and its source genome.

Accession
PA2386
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
pvdA pvd-1 PA2386
Status
annotated
Amino acids
443
3D evidence
Experimental + AlphaFold DB model
EC
1.14.13.195
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins. GO:0031172 Catalysis of the reaction: L-ornithine + O2 + H+ = N5-hydroxy-L-ornithine + H2O. GO:0006879 A homeostatic process involved in the maintenance of a steady state level of iron ions within a cell. GO:0002049 The chemical reactions and pathways resulting in the formation of the siderochrome pyoverdine.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected pocket evidence

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.725
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MTQATATAVVHDLIGVGFGPSNIALAIALQERAQAQGALEVLFLDKQGDYRWHGNTLVSQSELQISFLKDLVSLRNPTSPYSFVNYLHKHDRLVDFINLGTFYPCRMEFNDYLRWVASHFQEQSRYGEEVLRIEPMLSAGQVEALRVISRNADGEELVRTTRALVVSPGGTPRIPQVFRALKGDGRVFHHSQYLEHMAKQPCSSGKPMKIAIIGGGQSAAEAFIDLNDSYPSVQADMILRASALKPADDSPFVNEVFAPKFTDLIYSREHAERERLLREYHNTNYSVVDTDLIERIYGVFYRQKVSGIPRHAFRCMTTVERATATAQGIELALRDAGSGELSVETYDAVILATGYERQLHRQLLEPLAEYLGDHEIGRDYRLQTDERCKVAIYAQGFSQASHGLSDTLLSVLPVRAEEISGSLYQHLKPGTAARALHEHALAS

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0031172 Catalysis of the reaction: L-ornithine + O2 + H+ = N5-hydroxy-L-ornithine + H2O.
  • GO:0006879 A homeostatic process involved in the maintenance of a steady state level of iron ions within a cell.
  • GO:0002049 The chemical reactions and pathways resulting in the formation of the siderochrome pyoverdine.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
9 443 Gene3D G3DSA:3.50.50.60 -
9 443 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
10 357 Pfam PF13434 L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase
10 357 InterPro IPR025700 L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase
11 258 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
11 258 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
13 32 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
161 179 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
209 227 PRINTS PR00368 FAD-dependent pyridine nucleotide reductase signature
2 438 PANTHER PTHR42802 MONOOXYGENASE
2 438 InterPro IPR025700 L-lysine 6-monooxygenase/L-ornithine 5-monooxygenase
192 409 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
192 409 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

3D visualization script Full viewer

Loading 3D structure...

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Structural evidence

2 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 3S5W
X-ray 1.90 Å A,B
100.0% 1-443
PDBe RCSB PDBj File
Viewing
PDB 3S61
X-ray 3.03 Å A,B
100.0% 1-443
PDBe RCSB PDBj File
Loaded
AlphaFold DB PA2386
AlphaFold DB — — 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 0.725

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 54.37 0.984
2 2.51 0.07
3 2.24 0.055
4 1.76 0.032
5 1.7 0.03

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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 2 51 via homologs
Structural ligands 3 2 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 51 0 PAINS alerts
Best available ligand signal
ONH PDB co-crystal 148.2 Da · LogP -0.84 · TPSA 95.6 Open detail RCSB PDB
Detail RCSB PDB ONH PDB co-crystal
Detail RCSB PDB ORN PDB co-crystal
Detail RCSB PDB FDA PDB via homolog
Detail ZINC ZINC3055005 ZINC proposed compound · Tanimoto 0.750

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
ONH RCSB PDB
3S5W 1.90 Å Open crystal
148.2 Da LogP -0.84 TPSA 95.6 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)N)CNO
ORN RCSB PDB
3S61 3.03 Å Open crystal
132.2 Da LogP -0.86 TPSA 89.3 ✓ Ro5 ✓ Clean C(C[C@@H](C(=O)O)N)CN

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.