KpKP13 Protein target profile

p-hydroxybenzoate hydroxylase

Accession: KP13_32162

Gene: pobA AHE46475.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GIS2
Length 394
Pocket druggability (P2Rank · AlphaFold DB model) 0.92
Direct ligand evidence 0 62 total records
Functional annotation 1 EC 4 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
1.0% 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
97.09 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) 0.92
Structure A0A0H3GIS2
Pocket Pocket 1
Druggability (FPocket) 0.611
Structure A0A0H3GIS2
Pocket Pocket 9
ColabFold model
P2Rank 0.921 · Pocket 1
FPocket 0.585 · Pocket 10
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 48 / 4744 genomes with a hit
Prevalence 1.0%

Sequence

Primary amino-acid sequence viewer.

MKTQVAIIGAGPSGLLLGQLLHNAGIHTVILERQTPQYVLGRIRAGILESGTVDLLREAGVAQRMDAEGLVHHGVEFLFDGQRVPVALSELTDGKSVMVYGQTEVTRDLMAARAASGAPIVYGVSEVAIHDAKSDRPTITYLSEGETCRLECDFIAGCDGFHGVSRQSIPAGILQTYESVWPFGWLGLLADTPPVNPELIYAHHQRGFVLCSQRSLTRSRYYLQVPLSDKVEAWSDERFWQELKSRLPEELASRLVTGHSLEKSITPLRSFVVEPMQYGRLFLVGDAAHIVPPTGAKGLNLAASDVNYLWRILREYYHRGRSDLLAAYSQLALDRVWKGERFSWFMTRLLHDFPDQNAFDAKMQAADRRYYLGSRAGLTTIAENYVGLPTERVA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0043639 The chemical reactions and pathways resulting in the breakdown of benzoate, the anion of benzoic acid (benzenecarboxylic acid), a fungistatic compound widely used as a food preservative; it is conjugated to glycine in the liver and excreted as hippuric acid.
  • GO:0071949 Binding to the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
  • GO:0018659 Catalysis of the reaction: 4-hydroxybenzoate + NADPH + H+ + O2 = protocatechuate + NADP+ + H2O.
  • GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
1 389 NCBIfam TIGR02360 4-hydroxybenzoate 3-monooxygenase
1 389 InterPro IPR012733 4-hydroxybenzoate 3-monooxygenase
73 388 Gene3D G3DSA:3.30.9.10 -
2 329 PANTHER PTHR43004 TRK SYSTEM POTASSIUM UPTAKE PROTEIN
293 309 PRINTS PR00420 Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
310 328 PRINTS PR00420 Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
4 26 PRINTS PR00420 Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
151 166 PRINTS PR00420 Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
278 293 PRINTS PR00420 Aromatic-ring hydroxylase (flavoprotein monooxygenase) signature
1 388 SUPERFAMILY SSF51905 FAD/NAD(P)-binding domain
1 388 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
175 275 SUPERFAMILY SSF54373 FAD-linked reductases, C-terminal domain
2 351 Gene3D G3DSA:3.50.50.60 -
2 351 InterPro IPR036188 FAD/NAD(P)-binding domain superfamily
2 342 Pfam PF01494 FAD binding domain
2 342 InterPro IPR002938 FAD-binding domain

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
0.92
Likely same site as FPocket 13 6.2 Å 21 shared residues 91% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.039
Likely same site as FPocket 9 1.8 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.007
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #9
0.611
Likely same site as P2Rank 2 1.8 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #13
0.504
Likely same site as P2Rank 1 6.2 Å 21 shared residues 91% of smaller site
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_A0A0H3GIS2
AlphaFold DB full sequence Viewing
ColabFold KP13_32162
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.

62 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 12 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
APR PDB via homolog 559.3 Da · LogP -3.28 · TPSA 291.5 Open detail RCSB PDB
BHA PDB via homolog Detail RCSB PDB
DHB PDB via homolog Detail RCSB PDB
DOB PDB via homolog Detail RCSB PDB
FAS 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
APR RCSB PDB P00438 559.3 Da LogP -3.28 TPSA 291.5 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BHA RCSB PDB P00438 153.1 Da LogP 0.67 TPSA 83.5 ✓ Ro5 ✓ Clean c1cc(c(cc1N)O)C(=O)O
DHB RCSB PDB P20586 154.1 Da LogP 0.80 TPSA 77.8 ✓ Ro5 Alert c1cc(c(cc1C(=O)O)O)O
DOB RCSB PDB P20586 154.1 Da LogP 0.80 TPSA 77.8 ✓ Ro5 ✓ Clean c1cc(c(cc1O)O)C(=O)O
FAS RCSB PDB P00438 785.6 Da LogP -2.42 TPSA 362.9 3 viol. ✓ Clean Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@H]([C@@…
PAB RCSB PDB P20586 137.1 Da LogP 0.97 TPSA 63.3 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)O)N
PHB RCSB PDB C4TP09 138.1 Da LogP 1.09 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)O)O
PSL RCSB PDB P20586 176.1 Da LogP -2.08 TPSA 123.6 ✓ Ro5 ✓ Clean [O-]S(=O)(=O)OS(=O)(=O)[O-]
RFH RCSB PDB Q5YTV5 839.0 Da LogP 3.15 TPSA 248.0 2 viol. Alert Cc1c(c2c(c3c1O[C@](C3=O)(C)O/C=C/[C@@H]([C@@H](…
RFL RCSB PDB P20586 814.6 Da LogP -2.67 TPSA 366.2 3 viol. ✓ Clean Cc1cc2c(cc1N(C)C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]…
RFP RCSB PDB F2R776 823.0 Da LogP 4.34 TPSA 220.1 3 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…

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.