Protein target profile

VK055_0054

trehalose-phosphatase

Genome: KpATCC43816 Gene: otsB AIK78682.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 6 reactions UniProt A0A0H3GUW3

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Length 262

Pocket druggability 0.613

Metabolic reactions 6

Chokepoint No

Direct ligand evidence 0 53 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.

Main supporting evidence

No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. 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. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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: 1.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 34.783 Higher values support similarity to known essential genes.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 89.87 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.613

Structure A0A0H3GUW3

Pocket Pocket 3

P2Rank 0.19

Structure A0A0H3GUW3

Pocket Pocket 1

ColabFold model

FPocket 0.415 · Pocket 9

P2Rank 0.212 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 72 / 4744 genomes with a hit

Prevalence 1.5%

Cross-references

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

Sequence

UniProt A0A0H3GUW3

Pathways

BioCyc RXN1G-1438 BioCyc RXN1G-1435 BioCyc RXN1G-1437 KEGG R02778 BioCyc TREHALOSEPHOSPHA-RXN BioCyc RXN1G-1436 BioCyc RXN1G-1439

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

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MDNQISVPPALTGNYAFFFDLDGTLADIQPHPDQVVIPDSTLQALNALAQQQGGAVALISGRSMAELDALTHPWRLPLAGVHGAERRDINGKTYIVSLPTALRDEIAAELTSALEALPGCELESKEMAFALHYRQAPQQQSAVLELAQRIVQRYPLLALQLGKCVVEIKPRGVNKGEAITAFMQEAPFAGREPVFVGDDLTDEAGFSVVNQLQGMSVKVGAGETQAHWRLADAAAVRTWLQHLAYDAQTERRDDHESFSRSL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

3.1.3.12

Gene Ontology (GO)

GO:0005992 The chemical reactions and pathways resulting in the formation of trehalose, a disaccharide that consists of two molecules of glucose and is isomeric with sucrose.
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:0004805 Catalysis of the reaction: alpha,alpha-trehalose 6-phosphate + H2O = alpha,alpha-trehalose + phosphate.
GO:0000287 Binding to a magnesium (Mg) ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

14 records

Show feature table

Start	End	DB	Term	Name
16	244	SUPERFAMILY	SSF56784	HAD-like
16	244	InterPro	IPR036412	HAD-like superfamily
17	210	NCBIfam	TIGR01484	HAD-IIB family hydrolase
17	210	InterPro	IPR006379	HAD-superfamily hydrolase, subfamily IIB
15	244	NCBIfam	TIGR00685	trehalose-phosphatase
15	244	InterPro	IPR003337	Trehalose-phosphatase
99	171	Gene3D	G3DSA:3.30.70.1020	-
15	246	PANTHER	PTHR43768	TREHALOSE 6-PHOSPHATE PHOSPHATASE
15	246	InterPro	IPR044651	Trehalose 6-phosphate OTSB-like
18	230	Gene3D	G3DSA:3.40.50.1000	-
18	230	InterPro	IPR023214	HAD superfamily
16	237	CDD	cd01627	HAD_TPP
18	230	Pfam	PF02358	Trehalose-phosphatase
18	230	InterPro	IPR003337	Trehalose-phosphatase

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 · FPocket

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

Site 1 FPocket #3

0.613

Likely same site as P2Rank 2 5.2 Å 11 shared residues 69% of smaller site

Unusual size

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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

0.19

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Surrounding area

Site 2 P2Rank #2

0.176

Likely same site as FPocket 3 5.2 Å 11 shared residues 69% of smaller site

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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

0.212

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Surrounding area

Site 2 P2Rank #2

0.004

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Surrounding area

Site 3 P2Rank #3

0.003

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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_A0A0H3GUW3	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_0054	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.

53 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 3 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

BEF PDB via homolog 66.0 Da · LogP 0.88 · TPSA 0.0 Open detail RCSB PDB

OGS PDB via homolog Detail RCSB PDB

T6S PDB via homolog Detail RCSB PDB

ZINC13507434 ZINC proposed compound · Tanimoto 0.657 Detail ZINC

ZINC13551958 ZINC proposed compound · Tanimoto 0.657 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
BEF RCSB PDB	5DXI	Q5AI14	66.0 Da LogP 0.88 TPSA 0.0	✓ Ro5	✓ Clean	`[Be-](F)(F)F`
OGS RCSB PDB	6UPE	E1WGG9	448.5 Da LogP 1.60 TPSA 142.8	✓ Ro5	✓ Clean	`CCCCCCCCc1ccc(cc1)O[C@@H]2[C@@H]([C@H]([C@@H]([…`
T6S RCSB PDB	6UPC	E1WGG9	422.4 Da LogP -5.57 TPSA 232.9	2 viol.	✓ Clean	`C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@H]2[C…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC13507434 ZINC	0.657	260.2 Da LogP -3.39 TPSA 153.8	✓ Ro5	✓ Clean	`O=S(=O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C…`
ZINC13551958 ZINC	0.657	260.2 Da LogP -3.39 TPSA 153.8	✓ Ro5	✓ Clean	`O=S(=O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C…`
ZINC4095527 ZINC	0.657	260.2 Da LogP -3.39 TPSA 153.8	✓ Ro5	✓ Clean	`O=S(=O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC6753370 ZINC	0.657	260.2 Da LogP -3.39 TPSA 153.8	✓ Ro5	✓ Clean	`O=S(=O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[…`
ZINC16889851 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H…`
ZINC18033592 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@@H]2O[C@@H](CO)[C@H](O)[C@H…`
ZINC18045874 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O[C@H]2O[C@@H](CO)[C@@H](O)[C@…`
ZINC18166302 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@H]…`
ZINC18179993 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H…`
ZINC1857776326 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@H]2O[C@H](CO)[C@H](O)[C@@H]…`
ZINC1857776327 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@H]2O[C@H](CO)[C@H](O)[C@@H]…`
ZINC1857776328 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@H]2O[C@H](CO)[C@H](O)[C@@H]…`
ZINC1857776329 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@H]2O[C@H](CO)[C@H](O)[C@@H]…`
ZINC253497437 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@@H…`
ZINC253497438 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@@…`
ZINC253497439 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@H](O)[C@H]…`
ZINC253497440 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@H](O)[C@H…`
ZINC25723185 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O[C@@H]2O[C@@H](CO)[C@H](O)[C@…`
ZINC33834036 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H]…`
ZINC4095531 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H](…`
ZINC5225123 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O[C@H]2O[C@H](CO)[C@@H](O)[C@H…`
ZINC71789737 ZINC	0.656	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@H]2O[C@@H](CO)[C@H](O)[C@@H…`
ZINC71418197 ZINC	0.639	474.4 Da LogP -6.93 TPSA 248.4	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@H]2O[C@H](CO[C@H]3O[C@H](CO…`
ZINC15298193 ZINC	0.600	422.3 Da LogP -5.28 TPSA 236.1	2 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@H…`
ZINC1933262384 ZINC	0.600	422.3 Da LogP -5.28 TPSA 236.1	2 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@H…`
ZINC1933262385 ZINC	0.600	422.3 Da LogP -5.28 TPSA 236.1	2 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@H…`
ZINC1933262386 ZINC	0.600	422.3 Da LogP -5.28 TPSA 236.1	2 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@H]…`
ZINC1933262387 ZINC	0.600	422.3 Da LogP -5.28 TPSA 236.1	2 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@H]…`
ZINC256073272 ZINC	0.600	422.3 Da LogP -5.28 TPSA 236.1	2 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@H…`
ZINC256073273 ZINC	0.600	422.3 Da LogP -5.28 TPSA 236.1	2 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@…`
ZINC256073274 ZINC	0.600	422.3 Da LogP -5.28 TPSA 236.1	2 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@H…`
ZINC256073275 ZINC	0.600	422.3 Da LogP -5.28 TPSA 236.1	2 viol.	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O[C@@H]2O[C@H](CO)[C@@…`
ZINC4228300 ZINC	0.600	422.3 Da LogP -5.28 TPSA 236.1	2 viol.	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O[C@H]2O[C@H](CO)[C@@H]…`
ZINC96295928 ZINC	0.585	412.4 Da LogP -4.19 TPSA 195.6	2 viol.	✓ Clean	`CC(C)C(=O)OC[C@H]1O[C@H](O[C@H]2O[C@H](CO)[C@@H…`
ZINC32138054 ZINC	0.566	298.3 Da LogP -0.18 TPSA 99.4	✓ Ro5	✓ Clean	`CCCc1ccc(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O)[C@…`
ZINC107428582 ZINC	0.558	426.4 Da LogP -3.80 TPSA 195.6	2 viol.	✓ Clean	`CC[C@H](C)C(=O)OC[C@H]1O[C@H](O[C@H]2O[C@H](CO)…`
ZINC107428585 ZINC	0.558	426.4 Da LogP -3.80 TPSA 195.6	2 viol.	✓ Clean	`CC[C@@H](C)C(=O)OC[C@H]1O[C@H](O[C@H]2O[C@H](CO…`
ZINC100053716 ZINC	0.556	342.3 Da LogP -6.01 TPSA 200.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O)[C@H](O…`
ZINC100545802 ZINC	0.556	342.3 Da LogP -6.01 TPSA 200.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@H]2[C@H](O)[C@@H](O)[C@H](O)…`
ZINC257357488 ZINC	0.553	341.3 Da LogP -5.43 TPSA 195.3	2 viol.	✓ Clean	`N[C@H]1[C@@H](O)[C@H](CO)O[C@@H](O[C@H]2O[C@@H]…`
ZINC257357489 ZINC	0.553	341.3 Da LogP -5.43 TPSA 195.3	2 viol.	✓ Clean	`N[C@@H]1[C@H](O)[C@H](CO)O[C@@H](O[C@H]2O[C@@H]…`
ZINC257357490 ZINC	0.553	341.3 Da LogP -5.43 TPSA 195.3	2 viol.	✓ Clean	`N[C@@H]1[C@@H](O)[C@H](CO)O[C@@H](O[C@H]2O[C@@H…`
ZINC257357491 ZINC	0.553	341.3 Da LogP -5.43 TPSA 195.3	2 viol.	✓ Clean	`N[C@H]1[C@H](O)[C@H](CO)O[C@@H](O[C@H]2O[C@@H](…`
ZINC2042455763 ZINC	0.545	424.4 Da LogP -3.88 TPSA 195.6	2 viol.	✓ Clean	`C/C=C(\C)C(=O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)…`
ZINC2042455764 ZINC	0.545	424.4 Da LogP -3.88 TPSA 195.6	2 viol.	✓ Clean	`C/C=C(\C)C(=O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)…`
ZINC2042455765 ZINC	0.545	424.4 Da LogP -3.88 TPSA 195.6	2 viol.	✓ Clean	`C/C=C(\C)C(=O)OC[C@H]1O[C@H](O[C@@H]2O[C@H](CO)…`
ZINC38824035 ZINC	0.545	356.4 Da LogP 0.82 TPSA 108.6	✓ Ro5	✓ Clean	`CCCCCCOc1ccc(O[C@@H]2O[C@H](CO)[C@@H](O)[C@H](O…`
ZINC77257632 ZINC	0.545	424.4 Da LogP -3.88 TPSA 195.6	2 viol.	✓ Clean	`C/C=C(\C)C(=O)OC[C@H]1O[C@@H](O[C@H]2O[C@@H](CO…`
ZINC77257635 ZINC	0.545	424.4 Da LogP -3.88 TPSA 195.6	2 viol.	✓ Clean	`C/C=C(\C)C(=O)OC[C@H]1O[C@@H](O[C@H]2O[C@@H](CO…`
ZINC77257636 ZINC	0.545	424.4 Da LogP -3.88 TPSA 195.6	2 viol.	✓ Clean	`C/C=C(\C)C(=O)OC[C@@H]1O[C@@H](O[C@H]2O[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.