KpKP13 Protein target profile

Protocatechuate 3,4-dioxygenase alpha chain

Accession: KP13_04441

Gene: AHE44314.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GP30
Length 206
Pocket druggability (P2Rank · AlphaFold DB model) 0.094
Direct ligand evidence 0 68 total records
Functional annotation 0 EC 7 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on 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 Target 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.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
0.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
96.77 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.094
Structure A0A0H3GP30
Pocket Pocket 1
Druggability (FPocket) 0.538
Structure A0A0H3GP30
Pocket Pocket 1
ColabFold model
P2Rank 0.091 · Pocket 1
FPocket 0.527 · Pocket 8
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 37 / 4744 genomes with a hit
Prevalence 0.8%

Sequence

Primary amino-acid sequence viewer.

MKEYLPETASQTAGPYVHIGLAPDAAGFHIFEKNFGPVLTTADTAGERITIEGRVIDGSGTPVRDVLLEIWQANAAGRYNHPDDRQQQKAVDPAFRGWGRTCSDFTSGIWRFETIKPGPVAGRDGRLMAPHVNLWVVARGINIGLNTRMYFADEHEANASDPVLNLIEWEVRRKTLIAEREVRGTEVVYRFDIHLQGENETVFFDI

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

7
  • GO:0016702 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from one donor, and two oxygen atoms is incorporated into a donor.
  • GO:0018578 Catalysis of the reaction: 3,4-dihydroxybenzoate + O2 = 3-carboxy-cis,cis-muconate.
  • GO:0019439 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
  • GO:0006725 OBSOLETE. The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
  • GO:0005506 Binding to an iron (Fe) ion.
  • 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:0008199 Binding to a ferric iron ion, Fe(III).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
1 206 Gene3D G3DSA:2.60.130.10 Aromatic compound dioxygenase
1 206 InterPro IPR015889 Intradiol ring-cleavage dioxygenase, core
5 205 PANTHER PTHR33711 DIOXYGENASE, PUTATIVE (AFU_ORTHOLOGUE AFUA_2G02910)-RELATED
5 205 CDD cd03463 3,4-PCD_alpha
5 205 InterPro IPR012786 Protocatechuate 3,4-dioxygenase, alpha subunit
42 196 Pfam PF00775 Dioxygenase
42 196 InterPro IPR000627 Intradiol ring-cleavage dioxygenase, C-terminal
8 206 NCBIfam TIGR02423 protocatechuate 3,4-dioxygenase subunit alpha
8 206 InterPro IPR012786 Protocatechuate 3,4-dioxygenase, alpha subunit
3 206 SUPERFAMILY SSF49482 Aromatic compound dioxygenase
3 206 InterPro IPR015889 Intradiol ring-cleavage dioxygenase, core
51 79 ProSitePatterns PS00083 Intradiol ring-cleavage dioxygenases signature.
51 79 InterPro IPR000627 Intradiol ring-cleavage dioxygenase, C-terminal

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.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.094
Likely same site as FPocket 1 3.9 Å 8 shared residues 73% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.088
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Surrounding area
Pocket 3 P2Rank #3
0.007
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Surrounding area
Pocket 4 P2Rank #4
0.004
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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1
0.538
Likely same site as P2Rank 1 3.9 Å 8 shared residues 73% of smaller site
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Surrounding area
Pocket 2 FPocket #11
0.499
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

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 AF_A0A0H3GP30
AlphaFold DB full sequence Viewing
ColabFold KP13_04441
ColabFold full sequence Loaded

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.

68 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 18 records from similar proteins
Structural ligands 18 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3HB PDB via homolog 138.1 Da · LogP 1.09 · TPSA 57.5 Open detail RCSB PDB
3HP PDB via homolog Detail RCSB PDB
3N8 PDB via homolog Detail RCSB PDB
3N9 PDB via homolog Detail RCSB PDB
3NJ PDB via homolog Detail RCSB PDB

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
3HB RCSB PDB P00437 138.1 Da LogP 1.09 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(cc(c1)O)C(=O)O
3HP RCSB PDB P00436 152.1 Da LogP 1.02 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(cc(c1)O)CC(=O)O
3N8 RCSB PDB P00437 128.1 Da LogP 1.24 TPSA 40.5 ✓ Ro5 Alert c1cc(c(cc1F)O)O
3N9 RCSB PDB P00437 160.1 Da LogP 0.16 TPSA 66.8 ✓ Ro5 ✓ Clean C1=CC(=O)[C@@](C=C1F)(O)OO
3NJ RCSB PDB P00437 142.1 Da LogP 0.14 TPSA 47.3 ✓ Ro5 ✓ Clean C1=CC(=O)OC(=O)C=C1F
4HP RCSB PDB P00437 152.1 Da LogP 1.02 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(ccc1CC(=O)O)O
4NC RCSB PDB P00437 155.1 Da LogP 1.01 TPSA 83.6 ✓ Ro5 Alert c1cc(c(cc1[N+](=O)[O-])O)O
CAQ RCSB PDB P00437 110.1 Da LogP 1.10 TPSA 40.5 ✓ Ro5 Alert c1ccc(c(c1)O)O
CHB RCSB PDB P00437 172.6 Da LogP 1.74 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(c(cc1C(=O)O)Cl)O
DHB RCSB PDB P00437 154.1 Da LogP 0.80 TPSA 77.8 ✓ Ro5 Alert c1cc(c(cc1C(=O)O)O)O
DHY RCSB PDB P00437 168.1 Da LogP 0.72 TPSA 77.8 ✓ Ro5 Alert c1cc(c(cc1CC(=O)O)O)O
FHB RCSB PDB P00437 156.1 Da LogP 1.23 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(c(cc1C(=O)O)F)O
IHB RCSB PDB P00437 264.0 Da LogP 1.70 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(c(cc1C(=O)O)I)O
INO RCSB PDB P00437 155.1 Da LogP -0.28 TPSA 84.5 ✓ Ro5 ✓ Clean c1c[n+](c(cc1C(=O)O)O)[O-]
MUC RCSB PDB P00437 142.1 Da LogP -0.06 TPSA 63.6 ✓ Ro5 ✓ Clean C1=CC(=O)O[C@H]1CC(=O)O
NNO RCSB PDB P00437 155.1 Da LogP -0.28 TPSA 84.5 ✓ Ro5 ✓ Clean c1cc([n+](cc1C(=O)O)[O-])O
PHB RCSB PDB P00437 138.1 Da LogP 1.09 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)O)O
PTY RCSB PDB A4JR51 734.1 Da LogP 11.67 TPSA 134.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCCCCCC(=O)O[C@H](COC(=O)CCCCCCCCC…

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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.