Protein target profile

KP13_03756

Nucleoside permease nupC

Genome: KpKP13 Gene: AHE43371.1 nupC 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H172
Length 400
Pocket druggability 0.975
Direct ligand evidence 0 60 total records
Functional annotation 0 EC 7 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 (%)
26.478 Lower values reduce human off-target concern.
Human E-value
2.2000000000000004e-28
Gut microbiome similarity
3.6% 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
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
91.76 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 0.975
Structure A0A0H3H172
Pocket Pocket 2
P2Rank 0.795
Structure A0A0H3H172
Pocket Pocket 1
ColabFold model
FPocket 0.883 · Pocket 14
P2Rank 0.88 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 170 / 4744 genomes with a hit
Prevalence 3.6%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MDRVLHFVLAIVVVAILALLVSHDRQKIRIRYVVQLLVIEVLLAWFFLNSDIGLGFVKGFSEMFEKLLGFANEGTNFVFGGMNDKGLAFFFLKVLCPIVFISALIGILQHIRILPIVIRAIGTVLSKVNGMGKLESFNAVSSLILGQSENFIAYKDILGKMSRNRMYTMAATAMSTVSMSIVGAYMTMLQPKYVVAALVLNMFSTFIVLSLINPYRVEESEENLQMSNLHEGQSFFEMLGEYILAGFKVAIIVAAMLIGFIALISALNALFATVTGWFGYSISFQGILGYIFYPVAWVMGVPASEALQVGSIMATKLVSNEFVAMMDLQKIASTLSPRAEGIISIFLVSFANFSSIGIIAGAIKGLNEEQGNVVSRFGLKLVYGSTLVSVLSASIAALVL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0005337 Enables the transfer of a nucleoside, a nucleobase linked to either beta-D-ribofuranose (ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleotide) from one side of a membrane to the other.
  • GO:1901642 The directed movement of nucleoside across a membrane.
  • 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:0015212 Enables the transfer of cytidine, cytosine riboside, from one side of a membrane to the other.
  • GO:0015506 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: nucleoside(out) + H+(out) = nucleoside(in) + H+(in).
  • GO:0015213 Enables the transfer of uridine, uracil riboside, from one side of a membrane to the other.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

37 records
Show feature table
Start End DB Term Name
242 264 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
24 29 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
193 212 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
277 298 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
5 399 PANTHER PTHR10590 SODIUM/NUCLEOSIDE COTRANSPORTER
5 399 InterPro IPR008276 Concentrative nucleoside transporter
272 276 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
277 299 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
362 380 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
213 241 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
400 400 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
167 189 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
4 21 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
92 190 Pfam PF07670 Nucleoside recognition
92 190 InterPro IPR011642 Nucleoside transporter/FeoB GTPase, Gate domain
381 399 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
188 192 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
87 108 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
33 55 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
30 48 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
242 271 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
86 108 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
109 166 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
6 23 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
167 187 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
377 399 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
193 396 Pfam PF07662 Na+ dependent nucleoside transporter C-terminus
193 396 InterPro IPR011657 Concentrative nucleoside transporter C-terminal domain
299 340 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
10 82 Pfam PF01773 Na+ dependent nucleoside transporter N-terminus
10 82 InterPro IPR002668 Concentrative nucleoside transporter N-terminal domain
342 364 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
5 398 NCBIfam TIGR00804 NupC/NupG family nucleoside CNT transporter
5 398 InterPro IPR018270 Concentrative nucleoside transporter, metazoan/bacterial
341 361 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
49 86 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 #2
0.975
Likely same site as P2Rank 1 3.6 Å 15 shared residues 94% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #8
0.849
Likely same site as P2Rank 4 3.9 Å 10 shared residues 77% of smaller site
Show in viewer
Surrounding area
Site 3 FPocket #10
0.672
Likely same site as P2Rank 2 1.2 Å 12 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 4 FPocket #26
0.671
Likely same site as P2Rank 5 2.2 Å 10 shared residues 100% of smaller site
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.795
Likely same site as FPocket 2 3.6 Å 15 shared residues 94% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.283
Likely same site as FPocket 10 1.2 Å 12 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.203
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.202
Likely same site as FPocket 8 3.9 Å 10 shared residues 77% of smaller site
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.164
Likely same site as FPocket 26 2.2 Å 10 shared residues 100% 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_A0A0H3H172
AlphaFold DB full sequence Viewing
ColabFold KP13_03756
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.

60 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 10 records from similar proteins
Structural ligands 10 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5UD PDB via homolog 262.2 Da · LogP -2.71 · TPSA 124.8 Open detail RCSB PDB
6ZL PDB via homolog Detail RCSB PDB
ADN PDB via homolog Detail RCSB PDB
CTN PDB via homolog Detail RCSB PDB
DMU 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
5UD RCSB PDB Q9KPL5 262.2 Da LogP -2.71 TPSA 124.8 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)…
6ZL RCSB PDB G4CRQ5 949.1 Da LogP -3.24 TPSA 357.1 3 viol. ✓ Clean CCCCCCCCC(CCCCCCCC)(CO[C@H]1[C@@H]([C@H]([C@@H]…
ADN RCSB PDB Q9KPL5 267.2 Da LogP -1.98 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
CTN RCSB PDB Q9KPL5 243.2 Da LogP -2.56 TPSA 130.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
DMU RCSB PDB Q9KPL5 482.6 Da LogP -1.23 TPSA 178.5 2 viol. ✓ Clean CCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)C…
GEO RCSB PDB Q9KPL5 263.2 Da LogP -1.29 TPSA 110.6 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2C([C@@H]([C@H](O2)CO)O)(…
P0C RCSB PDB Q9KPL5 281.3 Da LogP -1.36 TPSA 120.6 ✓ Ro5 ✓ Clean CC1=CC2=CN(C(=O)N=C2N1)[C@H]3[C@@H]([C@@H]([C@H…
RBV RCSB PDB Q9KPL5 244.2 Da LogP -3.01 TPSA 143.7 ✓ Ro5 ✓ Clean c1nc(nn1[C@H]2[C@@H]([C@@H]([C@H](O2)CO)O)O)C(=…
URI RCSB PDB Q9KPL5 244.2 Da LogP -2.85 TPSA 124.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
ZE8 RCSB PDB Q9KPL5 228.2 Da LogP -2.15 TPSA 104.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1)[C@H]2[C@@H]([C@@H]([C@H](O2)CO…

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.