Protein target profile

VK055_1906

3-phytase

Genome: KpATCC43816 Gene: phyK AIK80512.1 3D evidence: Experimental + ColabFold model Metabolism 2 reactions UniProt Q84CN9
Length 421
Pocket druggability 0.725
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 56 total records
Functional annotation 1 EC 4 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
0.3% 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.

Localization

Localization
Periplasmic

Structure confidence

ColabFold pLDDT
94.52 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.725
Structure 2WNH
Pocket Pocket 11
P2Rank 0.784
Structure 2WNH
Pocket Pocket 1
ColabFold model
FPocket 0.378 · Pocket 6
P2Rank 0.726 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 15 / 4744 genomes with a hit
Prevalence 0.3%

Cross-references

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

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

2 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MPARHQGLLRLFIACALPLLALQSAAAADWQLEKVVELSRHGIRPPTAGNREAIEAATGRPWTEWTTHDGELTGHGYAAVVNKGRAEGQHYRQLGLLQAGCPTAESIYVRASPLQRTRATAQALVDGAFPGCGVAIHYVSGDADPLFQTDKFAATQTDPARQLAAVKEKAGDLAQRRQALAPTIQLLKQAVCQADKPCPIFDTPWQVEQSKSGKTTISGLSVMANMVETLRLGWSENLPLSQLAWGKITQARQITALLPLLTENYDLSNDVLYTAQKRGSVLLNAMLDGVKPEANPNVRWLLLVAHDTNIAMVRTLMNFSWQLPGYSRGNIPPGSSLVLERWRNAKSGERYLRVYFQAQGLDDLRRLQTPDAQHPMLRQEWRQPGCRQTDVGTLCPFQAAITALGQRIDRSSAPAVAMVLP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • GO:0016158 Catalysis of the reaction: myo-inositol hexakisphosphate + H2O = D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate.
  • GO:0046872 Binding to a metal ion.
  • GO:0050308 Catalysis of the reaction: sugar phosphate + H2O = sugar + phosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
1 10 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 27 Phobius SIGNAL_PEPTIDE Signal peptide region
28 421 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
23 27 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
28 408 SUPERFAMILY SSF53254 Phosphoglycerate mutase-like
28 408 InterPro IPR029033 Histidine phosphatase superfamily
11 22 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
32 46 ProSitePatterns PS00616 Histidine acid phosphatases phosphohistidine signature.
32 46 InterPro IPR033379 Histidine acid phosphatase active site
1 27 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
31 356 Pfam PF00328 Histidine phosphatase superfamily (branch 2)
31 356 InterPro IPR000560 Histidine phosphatase superfamily, clade-2
1 27 SignalP_EUK SignalP-noTM SignalP-noTM
26 359 PANTHER PTHR11567 ACID PHOSPHATASE-RELATED
31 357 CDD cd07061 HP_HAP_like
31 357 InterPro IPR000560 Histidine phosphatase superfamily, clade-2
20 421 Gene3D G3DSA:3.40.50.1240 -
20 421 InterPro IPR029033 Histidine phosphatase superfamily

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.

Download VMD script Full viewer

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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 · FPocket

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

Site 1 FPocket #11
0.725
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Surrounding area
Site 2 FPocket #23
0.504
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Surrounding area
Site 3 FPocket #1
0.484
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.784
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Surrounding area
Site 2 P2Rank #2
0.603
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Surrounding area
Site 3 P2Rank #3
0.053
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Surrounding area
Site 4 P2Rank #4
0.005
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Surrounding area
All structural evidence 3 experimental · 1 predicted

Structural evidence

3 + 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 2WNH
X-ray 1.68 Å A,B
93.3% 29-421
Viewing
PDB 2WNI
X-ray 2.57 Å A,B,C,D
93.3% 29-421
Loaded
PDB 2WU0
X-ray 2.57 Å A,B,C,D
93.3% 29-421
Loaded
ColabFold VK055_1906
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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
IHP PDB via homolog 660.0 Da · LogP -3.13 · TPSA 400.6 Open detail RCSB PDB
IHS PDB via homolog Detail RCSB PDB
P15 PDB via homolog Detail RCSB PDB
TLA PDB via homolog Detail RCSB PDB
TOE 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
IHP RCSB PDB P07102 660.0 Da LogP -3.13 TPSA 400.6 3 viol. ✓ Clean C1(C(C(C(C(C1OP(=O)(O)O)OP(=O)(O)O)OP(=O)(O)O)O…
IHS RCSB PDB H9TUK5 660.5 Da LogP -4.87 TPSA 381.6 3 viol. ✓ Clean C1(C(C(C(C(C1OS(=O)(=O)O)OS(=O)(=O)O)OS(=O)(=O)…
P15 RCSB PDB H9TUK6 296.4 Da LogP -0.29 TPSA 75.6 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCOCCO
TLA RCSB PDB H9TUK5 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O
TOE RCSB PDB H9TUK6 164.2 Da LogP -0.34 TPSA 47.9 ✓ Ro5 ✓ Clean COCCOCCOCCO
WO4 RCSB PDB P07102 247.8 Da LogP -2.62 TPSA 80.3 ✓ Ro5 ✓ Clean [O-][W](=O)(=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.