Protein target profile

KP13_03816

Uracil permease

Genome: KpKP13 Gene: uraA AHE43300.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWL3
Length 401
Pocket druggability 0.973
Direct ligand evidence 0 54 total records
Functional annotation 0 EC 5 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.

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 (%)
27.679 Lower values reduce human off-target concern.
Human E-value
1.42e-12
Gut microbiome similarity
11.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
40.106 Higher values support similarity to known essential genes.
DEG E-value
1.3199999999999998e-89 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
89.72 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 0.973
Structure A0A0H3GWL3
Pocket Pocket 1
P2Rank 0.334
Structure A0A0H3GWL3
Pocket Pocket 1
ColabFold model
FPocket 0.598 · Pocket 23
P2Rank 0.564 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 525 / 4744 genomes with a hit
Prevalence 11.1%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MFGATVLVPILFHINPATVLLFNGIGTLLYLFICKGKIPAYLGSSFAFISPVLLLLPLGYEVALGGFIMCGVLFCLVSFIVKKAGTGWLDVMFPPAAMGAIVAVIGLELAGVAANMAGLLPADGQSPDSKTIIISMVTLAVTVFGSVLFRGFLAIIPILIGVLVGYALSFVMGVVDTTPIAEAHWFALPTFYTPRFEWFAIFTILPAALVVIAEHVGHLVVTANIVKRDLIRDPGLHRSMFANGLSTIVSGFFGSTPNTTYGENIGVMAITRVYSTWVIGGAAIIAILLSCVGKLAAAIQIIPVPVMGGVSLLLYGVIGASGIRVLIESKVDYSKAQNLILTSVILIIGVSGAKVHIGAAELKGMALATIVGIALSLIFKLISVLRPEEVVLDAADSEEFK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0022857 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0042907 Enables the transfer of xanthine from one side of a membrane to the other. Xanthine (2,6-dihydroxypurine) is a purine formed in the metabolic breakdown of guanine, but is not present in nucleic acids.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
198 223 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
32 37 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
19 350 PANTHER PTHR42810 PURINE PERMEASE C1399.01C-RELATED
364 382 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
62 81 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
10 32 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
224 234 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
277 299 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
293 303 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
82 92 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
338 360 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
274 292 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
121 131 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
302 322 ProSitePatterns PS01116 Xanthine/uracil permeases family signature.
302 322 InterPro IPR006042 Xanthine/uracil permease
6 31 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
93 120 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
156 175 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
339 357 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
176 197 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
158 180 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
358 363 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
132 149 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
38 56 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
304 327 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
304 326 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
383 401 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
62 81 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
255 273 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
57 61 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
94 116 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
39 58 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
200 222 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
365 384 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 378 NCBIfam TIGR00801 NCS2 family nucleobase:cation symporter
1 378 InterPro IPR006042 Xanthine/uracil permease
1 356 Pfam PF00860 Permease family
1 356 InterPro IPR006043 Nucleobase cation symporter 2 family
131 153 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
150 155 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
235 254 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
328 338 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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 #1
0.973
Likely same site as P2Rank 1 1.7 Å 13 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #17
0.817
Likely same site as P2Rank 5 3.2 Å 8 shared residues 100% 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
0.334
Likely same site as FPocket 1 1.7 Å 13 shared residues 100% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.119
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Surrounding area
Site 3 P2Rank #3
0.114
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Surrounding area
Site 4 P2Rank #4
0.058
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Surrounding area
Site 5 P2Rank #5
0.05
Likely same site as FPocket 17 3.2 Å 8 shared residues 100% of smaller site
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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_A0A0H3GWL3
AlphaFold DB full sequence Viewing
ColabFold KP13_03816
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.

54 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 4 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
KEG PDB via homolog Open detail RCSB PDB
LMT PDB via homolog Detail RCSB PDB
URA PDB via homolog Detail RCSB PDB
XAN PDB via homolog Detail RCSB PDB
ZINC100053689 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
KEG RCSB PDB P0AGM8 O=[W]1234O[W]567(=O)O18[P]91O%10%11[W]%12%13(=O…
LMT RCSB PDB Q07307 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…
URA RCSB PDB P0AGM8 112.1 Da LogP -0.94 TPSA 65.7 ✓ Ro5 ✓ Clean C1=CNC(=O)NC1=O
XAN RCSB PDB Q07307 152.1 Da LogP -1.06 TPSA 94.4 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)C(=O)NC(=O)N2

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.