KpKP13 Protein target profile

PKHD-type hydroxylase

Accession: KP13_05370

Gene: AHE45016.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRM2
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Length 224
Pocket druggability (P2Rank · AlphaFold DB model) 0.887
Functional annotation 0 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.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.62. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.89. Review the complete evidence below

Risks to review

Microbiome similarity 57 of 4744 screened genomes (1.2%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.89) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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
1.2% 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
95.25 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) 0.887
Structure A0A0H3GRM2
Pocket Pocket 1
Druggability (FPocket) 0.621
Structure A0A0H3GRM2
Pocket Pocket 1
ColabFold model
P2Rank 0.897 · Pocket 1
FPocket 0.721 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 57 / 4744 genomes with a hit
Prevalence 1.2%

Sequence

Primary amino-acid sequence viewer.

MYHIPDVLSTDQVAEFTRQLAQAEWVDGRVTVGSQGAAVKQNQQIDTRTPLYARLQAAVLDMLRGHPQFFSAALPRTISAPLFNRYGPGETYGFHVDGAVRQNGEAGWMRTDLSATLFLCDPESYEGGELVIEDTYGQHRVKLPAGHLVLYPASSLHCVTPVTRGVRQASFLWIQSMVRDDKQRAMLYELDRTIQSLKARFGDGEEVLSLLNMYHNLLRQWTEV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

4
  • GO:0005506 Binding to an iron (Fe) ion.
  • GO:0016705 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
  • GO:0031418 Binding to L-ascorbic acid, (2R)-2-[(1S)-1,2-dihydroxyethyl]-4-hydroxy-5-oxo-2,5-dihydrofuran-3-olate; L-ascorbic acid is vitamin C and has co-factor and anti-oxidant activities in many species.
  • GO:0016706 Catalysis of the reaction: A + 2-oxoglutarate + O2 = B + succinate + CO2. This is an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from 2-oxoglutarate and one other donor, and one atom of oxygen is incorporated into each donor.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
1 175 SMART SM00702 p4hc
1 175 InterPro IPR006620 Prolyl 4-hydroxylase, alpha subunit
181 223 Pfam PF18331 PKHD-type hydroxylase C-terminal domain
181 223 InterPro IPR041097 PKHD-type hydroxylase C-terminal domain
77 176 ProSiteProfiles PS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.
77 176 InterPro IPR005123 Oxoglutarate/iron-dependent dioxygenase
1 224 PANTHER PTHR41536 PKHD-TYPE HYDROXYLASE YBIX
1 224 InterPro IPR023550 PKHD-type hydroxylase
178 224 Gene3D G3DSA:4.10.860.20 Rabenosyn, Rab binding domain
1 176 FunFam G3DSA:2.60.120.620:FF:000006 PKHD-type hydroxylase YbiX
83 174 Pfam PF13640 2OG-Fe(II) oxygenase superfamily
83 174 InterPro IPR044862 Prolyl 4-hydroxylase alpha subunit, Fe(2+) 2OG dioxygenase domain
1 224 Hamap MF_00657 PKHD-type hydroxylase YbiX [ybiX].
1 176 Gene3D G3DSA:2.60.120.620 q2cbj1_9rhob like 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
0.887
Likely same site as FPocket 1 1.0 Å 20 shared residues 95% of smaller site
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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
0.621 Unusual size
Likely same site as P2Rank 1 1.0 Å 20 shared residues 95% of smaller site
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Surrounding area
Pocket 2 FPocket #11
0.27
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:158-158
UniProt: Binding site:168-168
UniProt: Binding site:96-96
UniProt: Binding site:98-98
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_A0A0H3GRM2
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_05370
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GRM2