KpATCC43816 Protein target profile

uracil DNA glycosylase superfamily protein

Accession: VK055_3994

Gene: AIK82541.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GTH2

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Length 168

Pocket druggability (P2Rank · AlphaFold DB model) 0.819

Direct ligand evidence 0 16 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. Second pocket predictor agrees P2Rank predicted binding-site probability 0.82. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 2 structural and 0 bioactivity records.

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: Hit
Human identity (%): 47.5 Lower values reduce human off-target concern.
Human E-value: 6.66e-07
Gut microbiome similarity: 1.7% 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: 96.07 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) 0.819

Structure A0A0H3GTH2

Pocket Pocket 1

Druggability (FPocket) 0.868

Structure A0A0H3GTH2

Pocket Pocket 1

ColabFold model

P2Rank 0.822 · Pocket 1

FPocket 0.843 · Pocket 9

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 80 / 4744 genomes with a hit

Prevalence 1.7%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MISDILAPGLRVVFCGINPGKSSAHTGFHFAHPGNRFWKVIHQAGFTDRQLRPEEELQLLDTRCGITMLVERPTVQASEVALQELRSGGRELVRKIEEYQPQALAVLGKQAFELAFNQRGAKWGKQAMTIGTTQVWVLPNPSGLNRATLDKLVAAYRELDDALATRGQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization: Unknown

Enzyme Commission (EC)

3.2.2.28

Gene Ontology (GO)

GO:0000700 Catalysis of the removal of single bases present in mismatches by the cleavage the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.
GO:0006285 The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
GO:0008263 Catalysis of the removal of mismatched pyrimidine bases in DNA. Enzymes with this activity recognize and remove pyrimidines present in mismatches by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apyrimidinic (AP) site.
GO:0004844 Catalysis of the cleavage of the N-C1' glycosidic bond between the damaged DNA base and the deoxyribose sugar, releasing a free base and leaving an apyrimidinic (AP) site. Enzymes with this activity recognize and remove uracil bases in DNA that result from the deamination of cytosine or the misincorporation of dUTP opposite an adenine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
2	159	CDD	cd10028	UDG-F2_TDG_MUG
2	159	InterPro	IPR015637	Uracil DNA glycosylase family 2
6	159	Pfam	PF03167	Uracil DNA glycosylase superfamily
6	159	InterPro	IPR005122	Uracil-DNA glycosylase-like
1	168	Hamap	MF_01956	G/U mismatch-specific DNA glycosylase [mug].
1	168	InterPro	IPR023502	G/U mismatch-specific DNA glycosylase MUG, bacterial
3	159	SMART	SM00987	UDG_2_a
1	168	Gene3D	G3DSA:3.40.470.10	-
1	168	InterPro	IPR036895	Uracil-DNA glycosylase-like domain superfamily
2	162	PANTHER	PTHR12159	G/T AND G/U MISMATCH-SPECIFIC DNA GLYCOSYLASE
2	162	InterPro	IPR015637	Uracil DNA glycosylase family 2
3	159	SMART	SM00986	UDG_2
3	159	InterPro	IPR005122	Uracil-DNA glycosylase-like
2	161	SUPERFAMILY	SSF52141	Uracil-DNA glycosylase-like
2	161	InterPro	IPR036895	Uracil-DNA glycosylase-like domain 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.

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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

0.819

Likely same site as FPocket 1 2.5 Å 23 shared residues 96% 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

0.868 Unusual size

Likely same site as P2Rank 1 2.5 Å 23 shared residues 96% 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_A0A0H3GTH2	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_3994	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.

16 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 2 records from similar proteins

Structural ligands 2 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 14 similarity-based ZINC candidates

Best available ligand signal

1RT PDB via homolog 155.1 Da · LogP -0.95 · TPSA 109.1 Open detail RCSB PDB

HMU PDB via homolog Detail RCSB PDB

ZINC62714228 ZINC proposed compound · Tanimoto 0.613 Detail ZINC

ZINC1682039 ZINC proposed compound · Tanimoto 0.594 Detail ZINC

ZINC1615551 ZINC proposed compound · Tanimoto 0.586 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
1RT RCSB PDB	4JGC	Q13569	155.1 Da LogP -0.95 TPSA 109.1	✓ Ro5	✓ Clean	`C1=C(C(=NC(=O)N1)N)C(=O)O`
HMU RCSB PDB	4FNC	Q13569	142.1 Da LogP -1.44 TPSA 86.0	✓ Ro5	✓ Clean	`C1=C(C(=O)NC(=O)N1)CO`

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
ZINC62714228 ZINC	0.613	202.2 Da LogP -0.71 TPSA 85.9	✓ Ro5	✓ Clean	`O=c1[nH]cc(CSCCO)c(=O)[nH]1`
ZINC1682039 ZINC	0.594	229.2 Da LogP -2.15 TPSA 109.4	✓ Ro5	✓ Clean	`O=c1[nH]cc(CN(CCO)CCO)c(=O)[nH]1`
ZINC1615551 ZINC	0.586	314.3 Da LogP -2.45 TPSA 165.6	✓ Ro5	✓ Clean	`O=c1[nH]cc(CS(=O)(=O)Cc2c[nH]c(=O)[nH]c2=O)c(=O…`
ZINC95095499 ZINC	0.567	279.3 Da LogP -1.93 TPSA 134.7	✓ Ro5	✓ Clean	`CN(Cc1c[nH]c(=O)[nH]c1=O)Cc1c[nH]c(=O)[nH]c1=O`
ZINC967457 ZINC	0.567	237.0 Da LogP -0.04 TPSA 71.8	✓ Ro5	✓ Clean	`Nc1nc(=O)[nH]cc1I`
ZINC3682955 ZINC	0.545	218.2 Da LogP 0.36 TPSA 85.9	✓ Ro5	✓ Clean	`O=c1[nH]cc(Cc2ccc(O)cc2)c(=O)[nH]1`
ZINC1727445 ZINC	0.537	256.2 Da LogP -2.08 TPSA 158.4	✓ Ro5	✓ Clean	`C[C@H](O)[C@H](NC(=O)c1c[nH]c(=O)nc1N)C(=O)O`
ZINC1727446 ZINC	0.537	256.2 Da LogP -2.08 TPSA 158.4	✓ Ro5	✓ Clean	`C[C@@H](O)[C@H](NC(=O)c1c[nH]c(=O)nc1N)C(=O)O`
ZINC1727447 ZINC	0.537	256.2 Da LogP -2.08 TPSA 158.4	✓ Ro5	✓ Clean	`C[C@H](O)[C@@H](NC(=O)c1c[nH]c(=O)nc1N)C(=O)O`
ZINC1727448 ZINC	0.537	256.2 Da LogP -2.08 TPSA 158.4	✓ Ro5	✓ Clean	`C[C@@H](O)[C@@H](NC(=O)c1c[nH]c(=O)nc1N)C(=O)O`
ZINC1670654 ZINC	0.531	202.2 Da LogP 0.65 TPSA 65.7	✓ Ro5	✓ Clean	`O=c1[nH]cc(Cc2ccccc2)c(=O)[nH]1`
ZINC1734749 ZINC	0.515	216.2 Da LogP 0.85 TPSA 65.7	✓ Ro5	✓ Clean	`O=c1[nH]cc(CCc2ccccc2)c(=O)[nH]1`
ZINC2546072 ZINC	0.514	217.2 Da LogP 0.53 TPSA 95.9	✓ Ro5	✓ Clean	`O=C(O)c1c[nH]c(=O)nc1-c1ccncc1`
ZINC181793 ZINC	0.500	209.2 Da LogP 0.05 TPSA 69.0	✓ Ro5	✓ Clean	`O=c1[nH]cc(CN2CCCCC2)c(=O)[nH]1`

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.

Sequence

UniProt A0A0H3GTH2