Protein target profile

KP13_00801

Uracil-DNA glycosylase

Genome: KpKP13 Gene: AHE43166.1 ung 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GTU7
Length 237
Pocket druggability 0.357
Direct ligand evidence 0 67 total records
Functional annotation 1 EC 6 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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
Hit
Human identity (%)
64.848 Lower values reduce human off-target concern.
Human E-value
1.46e-72
Gut microbiome similarity
42.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
71.628 Higher values support similarity to known essential genes.
DEG E-value
3.34e-113 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.24 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 0.357
Structure A0A0H3GTU7
Pocket Pocket 5
P2Rank 0.429
Structure A0A0H3GTU7
Pocket Pocket 1
ColabFold model
FPocket 0.214 · Pocket 10
P2Rank 0.341 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 2006 / 4744 genomes with a hit
Prevalence 42.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MTLLQESKMTTPLTWHDVLADEKQQPYFLNTLKTVAEERQSGITIYPPQKDVFNAFRFTELGDVKVVILGQDPYHGPGQAHGLAFSVRPGVAIPPSLLNMYKELEATIPGFTRPTHGYLESWARQGVLLLNTVLTVRAGQAHSHASLGWETFTDKVIALINEHCEGVVFLLWGSHAQKKGAIIDRQRHCVLKAPHPSPLSAHRGFFGCNHFVQTNQWLVDRGETPIDWMPVLPAESE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0006284 In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
  • 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.
  • GO:0016799 Catalysis of the hydrolysis of any N-glycosyl bond.
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0097510 A base-excision repair, AP site formation process occurring via excision of a deaminated base.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
11 237 Gene3D G3DSA:3.40.470.10 -
11 237 InterPro IPR036895 Uracil-DNA glycosylase-like domain superfamily
57 218 SMART SM00987 UDG_2_a
27 228 CDD cd10027 UDG-F1-like
27 228 InterPro IPR002043 Uracil-DNA glycosylase family 1
57 218 SMART SM00986 UDG_2
57 218 InterPro IPR005122 Uracil-DNA glycosylase-like
12 228 SUPERFAMILY SSF52141 Uracil-DNA glycosylase-like
12 228 InterPro IPR036895 Uracil-DNA glycosylase-like domain superfamily
5 232 FunFam G3DSA:3.40.470.10:FF:000001 Uracil-DNA glycosylase
14 221 NCBIfam TIGR00628 uracil-DNA glycosylase
14 221 InterPro IPR002043 Uracil-DNA glycosylase family 1
12 229 Hamap MF_00148 Uracil-DNA glycosylase [ung].
12 229 InterPro IPR002043 Uracil-DNA glycosylase family 1
4 230 PANTHER PTHR11264 URACIL-DNA GLYCOSYLASE
4 230 InterPro IPR002043 Uracil-DNA glycosylase family 1
65 74 ProSitePatterns PS00130 Uracil-DNA glycosylase signature.
65 74 InterPro IPR018085 Uracil-DNA glycosylase, active site
63 217 Pfam PF03167 Uracil DNA glycosylase superfamily
63 217 InterPro IPR005122 Uracil-DNA glycosylase-like

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 #5
0.357
Likely same site as P2Rank 3 2.4 Å 3 shared residues 75% of smaller site
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Surrounding area
Site 2 FPocket #3
0.252
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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
0.429
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.012
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.012
Likely same site as FPocket 5 2.4 Å 3 shared residues 75% of smaller site
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Surrounding area
Site 4 P2Rank #4
0.004
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Surrounding area
Residue sets
UniProt: Active site:64-64 Proton acceptor
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_A0A0H3GTU7
AlphaFold DB full sequence Viewing
ColabFold KP13_00801
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.

67 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 17 records from similar proteins
Structural ligands 16 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
302 PDB via homolog 346.3 Da · LogP 0.16 · TPSA 146.2 Open detail RCSB PDB
3FI PDB via homolog Detail RCSB PDB
3FL PDB via homolog Detail RCSB PDB
5NU PDB via homolog Detail RCSB PDB
5UC 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
302 RCSB PDB P13051 346.3 Da LogP 0.16 TPSA 146.2 ✓ Ro5 ✓ Clean c1cc(ccc1\C=N\OCCO/N=C/C2=CC(=O)NC(=O)N2)C(=O)O
3FI RCSB PDB P13051 346.3 Da LogP 0.29 TPSA 136.6 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(=O)O)\C=N\OCCCNCC2=CC(=O)NC(=O)N2
3FL RCSB PDB P13051 346.4 Da LogP 0.42 TPSA 127.1 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(=O)O)CNCCCCNCC2=CC(=O)NC(=O)N2
5NU RCSB PDB P9WFQ9 157.1 Da LogP -1.03 TPSA 108.9 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1)[N+](=O)[O-]
5UC RCSB PDB P9WFQ9 146.5 Da LogP -0.28 TPSA 65.7 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1)Cl
6UA RCSB PDB P9WFQ9 127.1 Da LogP -1.02 TPSA 84.5 ✓ Ro5 ✓ Clean C1C(=NC(=O)NC1=O)N
DUR RCSB PDB P10186 228.2 Da LogP -1.82 TPSA 104.6 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO)O
FCF RCSB PDB P13051 346.3 Da LogP 0.16 TPSA 146.2 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(=O)O)\C=N\OCCO/N=C/C2=CC(=O)NC(=O)…
FCK RCSB PDB P13051 346.3 Da LogP 0.29 TPSA 136.6 ✓ Ro5 ✓ Clean c1cc(cc(c1)C(=O)O)CNCCCON=CC2=CC(=O)NC(=O)N2
FLC RCSB PDB P9WFQ9 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
QU4 RCSB PDB P13051 422.3 Da LogP 2.45 TPSA 169.4 ✓ Ro5 ✓ Clean c1cc(c(cc1C(=C2C=CC(=O)C(=C2)C(=O)O)c3ccc(c(c3)…
TUL RCSB PDB P9WFQ9 128.2 Da LogP 0.43 TPSA 48.6 ✓ Ro5 ✓ Clean C1=CNC(=S)NC1=O
URA RCSB PDB P12295 112.1 Da LogP -0.94 TPSA 65.7 ✓ Ro5 ✓ Clean C1=CNC(=O)NC1=O
URB RCSB PDB D0VWU0 191.0 Da LogP -0.17 TPSA 65.7 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1)Br
URF RCSB PDB P9WFQ9 130.1 Da LogP -0.80 TPSA 65.7 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1)F
WBU RCSB PDB P9WFQ9 127.1 Da LogP -1.35 TPSA 91.7 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1)N

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.