Protein target profile

PA2516

toluate 1,2-dioxygenase electron transfer subunit

Genome: NC_002516.2

Gene: PA2516 xylZ 3D evidence: AlphaFold DB model UniProt Q9I0W6
Length 337
Pocket druggability 0.732
Ligand records 57
EC / GO 0 / 3
Target summary

Promising target candidate with multiple supporting evidence streams.

5 signals
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
PA2516
Gene
PA2516 xylZ
Status
annotated
Amino acids
337
3D evidence
AlphaFold DB model

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 0.732
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MNHRIALNFEDGVTRFIHAAPGETVADAAYRQGINIPLDCRDGACGTCKCLAEAGRYALGQDYIDDALSAEEAARGYVLTCQMRAESDCVLRVPASSTLCRTGQARYEARISEVRQLSPSTIGLSLRGEALASLAFLPGQYVNLQVPGSEQRRAYSFSSLAKDGEVSFLIRNVPGGLMSGFLSGTARAGDSLAMDGPLGSFYLREIHRPLLMLAGGTGLAPFTAMLERIAEQGSAHPLHLVYGVTHDVDLVGLERLEAFAERIPGFTWSACVASADSDYPRKGYVTEHIAAQHLHEGDVDIYLCGPPPMVEAVERYLREQGVRPANFYYEKFAASAA

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

3
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.

Sequence Features

Domain/signature hits from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
10 85 Pfam PF00111 2Fe-2S iron-sulfur cluster binding domain
10 85 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain
1 100 Gene3D G3DSA:3.10.20.30 -
1 100 InterPro IPR012675 Beta-grasp domain superfamily
204 333 SUPERFAMILY SSF52343 Ferredoxin reductase-like, C-terminal NADP-linked domain
204 333 InterPro IPR039261 Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
104 204 ProSiteProfiles PS51384 Ferredoxin reductase-type FAD binding domain profile.
104 204 InterPro IPR017927 FAD-binding domain, ferredoxin reductase-type
40 48 ProSitePatterns PS00197 2Fe-2S ferredoxin-type iron-sulfur binding region signature.
40 48 InterPro IPR006058 2Fe-2S ferredoxin, iron-sulphur binding site
3 335 NCBIfam NF040810 benzoate 1,2-dioxygenase electron transfer component BenC
196 205 PRINTS PR00410 Phenol hydroxylase reductase family signature
211 230 PRINTS PR00410 Phenol hydroxylase reductase family signature
136 148 PRINTS PR00410 Phenol hydroxylase reductase family signature
153 160 PRINTS PR00410 Phenol hydroxylase reductase family signature
236 245 PRINTS PR00410 Phenol hydroxylase reductase family signature
300 308 PRINTS PR00410 Phenol hydroxylase reductase family signature
106 333 CDD cd06209 BenDO_FAD_NAD
106 333 InterPro IPR047683 Benzoate 1,2-dioxygenase reductase, FAD/NAD binding domain
3 97 ProSiteProfiles PS51085 2Fe-2S ferredoxin-type iron-sulfur binding domain profile.
3 97 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain
101 199 Gene3D G3DSA:2.40.30.10 Translation factors
153 160 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
153 160 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
236 245 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
236 245 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
211 230 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
211 230 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
300 308 PRINTS PR00371 Flavoprotein pyridine nucleotide cytochrome reductase signature
300 308 InterPro IPR001709 Flavoprotein pyridine nucleotide cytochrome reductase
17 92 CDD cd00207 fer2
17 92 InterPro IPR001041 2Fe-2S ferredoxin-type iron-sulfur binding domain
109 202 Pfam PF00970 Oxidoreductase FAD-binding domain
109 202 InterPro IPR008333 Flavoprotein pyridine nucleotide cytochrome reductase-like, FAD-binding domain
1 98 SUPERFAMILY SSF54292 2Fe-2S ferredoxin-like
1 98 InterPro IPR036010 2Fe-2S ferredoxin-like superfamily
76 204 SUPERFAMILY SSF63380 Riboflavin synthase domain-like
76 204 InterPro IPR017938 Riboflavin synthase-like beta-barrel
200 332 Gene3D G3DSA:3.40.50.80 -
200 332 InterPro IPR039261 Ferredoxin-NADP reductase (FNR), nucleotide-binding domain
212 314 Pfam PF00175 Oxidoreductase NAD-binding domain
212 314 InterPro IPR001433 Oxidoreductase FAD/NAD(P)-binding
17 91 PANTHER PTHR47354 NADH OXIDOREDUCTASE HCR

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

0 + 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
AlphaFold DB PA2516
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 0.732

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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 57 via homologs
Structural ligands 7 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 48 5 PAINS alerts
Best available ligand signal
BTB PDB via homolog 209.2 Da · LogP -3.01 · TPSA 104.4 Open detail RCSB PDB
Detail RCSB PDB BTB PDB via homolog
Detail RCSB PDB DGG PDB via homolog
Detail RCSB PDB ECN PDB via homolog
Detail RCSB PDB FDA 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
BTB RCSB PDB Q03304 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
DGG RCSB PDB P39662 735.0 Da LogP 9.75 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](CO[P@@](=O)(O)OC[C@…
ECN RCSB PDB P39662 381.7 Da LogP 5.80 TPSA 27.1 1 viol. ✓ Clean c1cc(ccc1COC(Cn2ccnc2)c3ccc(cc3Cl)Cl)Cl
FDA RCSB PDB P22868 787.6 Da LogP -1.75 TPSA 363.3 3 viol. ✓ Clean Cc1cc2c(cc1C)N(C3=C(N2)C(=O)NC(=O)N3)C[C@@H]([C…
FES RCSB PDB A0A076MZ01 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
KKK RCSB PDB P39662 531.4 Da LogP 4.21 TPSA 69.1 1 viol. Alert CC(=O)N1CCN(CC1)c2ccc(cc2)OC[C@H]3CO[C@](O3)(Cn…
X89 RCSB PDB P39662 416.1 Da LogP 6.45 TPSA 27.1 1 viol. ✓ Clean c1cc(c(cc1Cl)Cl)CO[C@@H](Cn2ccnc2)c3ccc(cc3Cl)Cl

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.