Protein target profile

PA1904

trans-2,3-dihydro-3-hydroxyanthranilate isomerase

Genome: NC_002516.2

Gene: PA4215 phzF1 phzF phzF2 PA1904; 3D evidence: AlphaFold DB model UniProt O69754
Export view
Length 278
Pocket druggability 0.669
Ligand records 55
EC / GO 0 / 2
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

3 signals

Strengths

Moderate predicted binding pocket FPocket selected-pocket score 0.67. This supports review but is not experimental validation. Structure available AlphaFold DB model Ligand evidence via structure/bioactivity 5 structural and 0 bioactivity records.

Risks / watch

Human similarity Top human hit identity: 27.984%.

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
PA1904
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA4215 phzF1 phzF phzF2 PA1904;
Status
annotated
Amino acids
278
3D evidence
AlphaFold DB model
GO
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:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
27.984
Human E-value
2.08e-10
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 0.669
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MHRYVVIDAFASEPLQGNPVAVFFDCDDLSGERMQRMAREMNLSESTFVLRPQQDGDARIRIFTPVNELPFAGHPLLGTAIALGAETDKDRLFLETRMGTVPFALERQDGKVVACSMQQPIPTWEHFSRPAELLAALGLKGSTFPIEVYRNGPRHVFVGLESVAALSALHPDHRALCDFPDLAVNCFAGAGRHWRSRMFSPAYGVVEDAATGSAAGPLAIHLARHRQIPYGQQIEILQGVEIGRPSRMYARAEGAGERVSAVEVSGNGAAFAEGRAYL

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Gene Ontology (GO)

2
  • 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:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
1 278 PIRSF PIRSF016184 Ismrse_PhzF
1 278 InterPro IPR003719 Phenazine biosynthesis PhzF-like
120 266 Gene3D G3DSA:3.10.310.10 Diaminopimelate Epimerase; Chain A, domain 1
3 275 PANTHER PTHR13774 PHENAZINE BIOSYNTHESIS PROTEIN
3 275 InterPro IPR003719 Phenazine biosynthesis PhzF-like
7 119 Gene3D G3DSA:3.10.310.10 Diaminopimelate Epimerase; Chain A, domain 1
5 273 NCBIfam TIGR00654 PhzF family phenazine biosynthesis isomerase
5 273 InterPro IPR003719 Phenazine biosynthesis PhzF-like
2 277 SUPERFAMILY SSF54506 Diaminopimelate epimerase-like
7 274 Pfam PF02567 Phenazine biosynthesis-like protein
7 274 InterPro IPR003719 Phenazine biosynthesis PhzF-like

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

5 + 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 9F96
X-ray 1.27 Å A
100.0% 1-278
PDBe RCSB PDBj File
Metadata only
PDB 9F92
X-ray 1.32 Å A
100.0% 1-278
PDBe RCSB PDBj File
Metadata only
PDB 9F94
X-ray 1.32 Å A
100.0% 1-278
PDBe RCSB PDBj File
Metadata only
PDB 9F95
X-ray 1.46 Å A
100.0% 1-278
PDBe RCSB PDBj File
Metadata only
PDB 9F93
X-ray 1.54 Å A
100.0% 1-278
PDBe RCSB PDBj File
Metadata only
AlphaFold DB PA1904
AlphaFold DB — — 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 0.669
2 0.368

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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 55 via homologs
Structural ligands 5 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 54 1 PAINS alerts
Best available ligand signal
3HA PDB via homolog 153.1 Da · LogP 0.67 · TPSA 83.5 Open detail RCSB PDB
Detail RCSB PDB 3HA PDB via homolog
Detail RCSB PDB BTB PDB via homolog
Detail RCSB PDB HHA PDB via homolog
Detail RCSB PDB SIN PDB via homolog

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
3HA RCSB PDB
1U1W
Q51792 153.1 Da LogP 0.67 TPSA 83.5 ✓ Ro5 ✓ Clean c1cc(c(c(c1)O)N)C(=O)O
BTB RCSB PDB
4DUN
Q186X0 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
HHA RCSB PDB
1U1X
Q51792 155.2 Da LogP -0.74 TPSA 83.5 ✓ Ro5 ✓ Clean C1=C[C@@H]([C@H](C(=C1)C(=O)O)N)O
SIN RCSB PDB
3EDN
A0A6L8PH16 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
W81 RCSB PDB
5IWE
Q51792 183.2 Da LogP -1.75 TPSA 77.0 ✓ Ro5 ✓ Clean CCO[C@@H]1C=CC=C([C@H]1[NH3+])C(=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.