Protein target profile

KP13_00302

Cytoplasmic trehalase

Genome: KpKP13 Gene: treF AHE42212.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GYL8

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Length 550

Pocket druggability 0.654

Direct ligand evidence 0 11 total records

Functional annotation 1 EC 6 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

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.65. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.90. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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: Hit
Human identity (%): 34.221 Lower values reduce human off-target concern.
Human E-value: 6.2e-75
Gut microbiome similarity: 1.6% 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: Cytoplasmic

Structure confidence

ColabFold pLDDT: 90.89 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 0.654

Structure A0A0H3GYL8

Pocket Pocket 4

P2Rank 0.904

Structure A0A0H3GYL8

Pocket Pocket 1

ColabFold model

FPocket 0.352 · Pocket 23

P2Rank 0.858 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 76 / 4744 genomes with a hit

Prevalence 1.6%

Cross-references

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

Sequence

UniProt A0A0H3GYL8

Chemistry

ChEMBL VDM ChEMBL CHEMBL2270892 ChEMBL CHEMBL145196

Sequence

Primary amino-acid sequence viewer.

MFSQKLRHVEDDELRIDIDPCYEADPYELKLDEMIDAEPEPEVIEGLPASDALTPADRYLELFTNVQKSRIFADSKTFPDCAPKHDPLDILRNYRKVKRQPDFDLRQFVEDNFWLPESQSDIYISDPSLTLKEHIDKLWPVLTREPQDHIPWSSLLALPQAYIVPGGRFSETYYWDSYFTMLGLAESGREDLLKCMADNFAWLIETYGHIPNGNRTYYLSRSQPPVFALMVELFEEDGVRGAKRYLDHLKMEHAFWMDGAESLIPHQAYRHVVRMPDGSLLNRYWDDRDTPRDESWREDVETARHSGRPANEVYRDLRAGAASGWDYSSRWLRDITRLASIRTTQFIPIDLNAFLFKLETTIANLSGLKGDRETEAAFRQKAQDRRAAVNRYLWDDENGCFRDYDWRREQLALFSAASIVTLYVGLATHEQAERLADAVRARLLTPGGIMATEYESGEQWDKPNGWAPLQWMAIQGFKRYGQDPLGDEIAWSWLQTVNHFYKQHHKLIEKYHIATGVPHEGGGGEYPLQDGFGWTNGVVRRLIGLYGEPT

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

3.2.1.28

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005975 The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y.
GO:0071474 Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of detection of, or exposure to, a hyperosmotic environment, i.e. an environment with a higher concentration of solutes than the organism or cell.
GO:0005991 The chemical reactions and pathways involving trehalose, a disaccharide that consists of two molecules of glucose and is isomeric with sucrose.
GO:0004555 Catalysis of the reaction: alpha,alpha-trehalose + H2O = 2 D-glucose.
GO:0005993 The chemical reactions and pathways resulting in the breakdown of trehalose, a disaccharide that consists of two molecules of glucose and is isomeric with sucrose.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

29 records

Show feature table

Start	End	DB	Term	Name
54	549	FunFam	G3DSA:1.50.10.10:FF:000003	Cytoplasmic trehalase
54	549	Gene3D	G3DSA:1.50.10.10	-
54	549	InterPro	IPR012341	Six-hairpin glycosidase-like superfamily
61	549	PANTHER	PTHR23403	TREHALASE
61	549	InterPro	IPR001661	Glycoside hydrolase, family 37
34	549	Hamap	MF_01059	Cytoplasmic trehalase [treF].
34	549	InterPro	IPR023715	Trehalase, cytoplasmic
55	547	SUPERFAMILY	SSF48208	Six-hairpin glycosidases
55	547	InterPro	IPR008928	Six-hairpin glycosidase superfamily
165	178	ProSitePatterns	PS00927	Trehalase signature 1.
165	178	InterPro	IPR018232	Glycoside hydrolase, family 37, conserved site
452	468	PRINTS	PR00744	Glycosyl hydrolase family 37 signature
452	468	InterPro	IPR001661	Glycoside hydrolase, family 37
389	405	PRINTS	PR00744	Glycosyl hydrolase family 37 signature
389	405	InterPro	IPR001661	Glycoside hydrolase, family 37
346	363	PRINTS	PR00744	Glycosyl hydrolase family 37 signature
346	363	InterPro	IPR001661	Glycoside hydrolase, family 37
281	298	PRINTS	PR00744	Glycosyl hydrolase family 37 signature
281	298	InterPro	IPR001661	Glycoside hydrolase, family 37
314	331	PRINTS	PR00744	Glycosyl hydrolase family 37 signature
314	331	InterPro	IPR001661	Glycoside hydrolase, family 37
530	543	PRINTS	PR00744	Glycosyl hydrolase family 37 signature
530	543	InterPro	IPR001661	Glycoside hydrolase, family 37
207	225	PRINTS	PR00744	Glycosyl hydrolase family 37 signature
207	225	InterPro	IPR001661	Glycoside hydrolase, family 37
459	468	ProSitePatterns	PS00928	Trehalase signature 2.
459	468	InterPro	IPR018232	Glycoside hydrolase, family 37, conserved site
71	546	Pfam	PF01204	Trehalase
71	546	InterPro	IPR001661	Glycoside hydrolase, family 37

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 #4

0.654

Unusual size

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Surrounding area

Site 2 FPocket #5

0.224

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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

0.904

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Surrounding area

Site 2 P2Rank #2

0.533

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Surrounding area

Site 3 P2Rank #3

0.189

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Surrounding area

Site 4 P2Rank #4

0.147

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Surrounding area

Site 5 P2Rank #5

0.07

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Surrounding area

Residue sets

UniProt: Active site:326-326 Proton donor/acceptor

UniProt: Active site:509-509 Proton donor/acceptor

UniProt: Binding site:168-168

UniProt: Binding site:175-176

UniProt: Binding site:212-212

UniProt: Binding site:221-223

UniProt: Binding site:292-294

UniProt: Binding site:324-324

UniProt: Binding site:525-525

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.858

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Surrounding area

Site 2 P2Rank #2

0.329

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Surrounding area

Site 3 P2Rank #3

0.223

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Surrounding area

Site 4 P2Rank #4

0.223

Likely same site as FPocket 23 4.1 Å 18 shared residues 90% of smaller site

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Surrounding area

Site 5 P2Rank #5

0.101

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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_A0A0H3GYL8	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_00302	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.

11 records

Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records

Transferred evidence 4 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 3 direct and transferred ChEMBL records

Proposed compounds 7 similarity-based ZINC candidates

Best available ligand signal

3CU PDB via homolog 205.2 Da · LogP -3.51 · TPSA 104.4 Open detail RCSB PDB

VDM ChEMBL via homolog · pchembl 8.31 (~4.9 nM) Detail ChEMBL

CHEMBL2270892 ChEMBL via homolog · pchembl 7.31 (~49.0 nM) Detail ChEMBL

CHEMBL145196 ChEMBL via homolog · pchembl 6.75 (~177.8 nM) Detail ChEMBL

ZINC1857787936 ZINC proposed compound · Tanimoto 0.647 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
3CU RCSB PDB	2JJB	P13482	205.2 Da LogP -3.51 TPSA 104.4	✓ Ro5	✓ Clean	`C1[C@@H]([C@H]([C@H]2[N@@]1[C@@H]([C@H]([C@@H]2…`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
VDM ChEMBL	O70282	8.31 ~4.9 nM	335.4 Da LogP -4.58 TPSA 173.9	1 viol.	✓ Clean	`C1[C@@H]([C@H]([C@@H]([C@H]([C@H]1N[C@H]2C=C([C…`
CHEMBL2270892 ChEMBL	P32358	7.31 ~49.0 nM	366.3 Da LogP -6.04 TPSA 204.7	2 viol.	✓ Clean	`OC[C@H]1O[C@H](NC2=N[C@@H]3[C@H](O2)[C@@H](O)[C…`
CHEMBL145196 ChEMBL	O43280	6.75 ~177.8 nM	321.3 Da LogP -4.56 TPSA 162.9	1 viol.	✓ Clean	`OCC1=CC(NC2COC(CO)C(O)C2O)C(O)C(O)C1O`

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
ZINC1857787936 ZINC	0.647	497.5 Da LogP -6.75 TPSA 253.0	2 viol.	✓ Clean	`OCC1=C[C@@H](N[C@@H]2C[C@@H](CO)[C@H](O[C@H]3O[…`
ZINC2053528368 ZINC	0.647	497.5 Da LogP -6.75 TPSA 253.0	2 viol.	✓ Clean	`OCC1=C[C@@H](N[C@@H]2C[C@H](CO)[C@@H](O[C@H]3O[…`
ZINC2053528371 ZINC	0.647	497.5 Da LogP -6.75 TPSA 253.0	2 viol.	✓ Clean	`OCC1=C[C@@H](N[C@@H]2C[C@H](CO)[C@@H](O[C@H]3O[…`
ZINC2053528373 ZINC	0.647	497.5 Da LogP -6.75 TPSA 253.0	2 viol.	✓ Clean	`OCC1=C[C@@H](N[C@@H]2C[C@H](CO)[C@@H](O[C@H]3O[…`
ZINC2053528375 ZINC	0.647	497.5 Da LogP -6.75 TPSA 253.0	2 viol.	✓ Clean	`OCC1=C[C@@H](N[C@@H]2C[C@H](CO)[C@@H](O[C@H]3O[…`
ZINC8437016 ZINC	0.647	497.5 Da LogP -6.75 TPSA 253.0	2 viol.	✓ Clean	`OCC1=C[C@H](N[C@H]2C[C@H](CO)[C@@H](O[C@@H]3O[C…`
ZINC16052241 ZINC	0.600	335.4 Da LogP -4.58 TPSA 173.9	1 viol.	✓ Clean	`OCC1=C[C@H](N[C@H]2C[C@H](CO)[C@@H](O)[C@H](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.