Protein target profile

KP13_03903

Putrescine importer

Genome: KpKP13 Gene: puuP AHE45351.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GL69
Length 463
Pocket druggability 0.989
Direct ligand evidence 0 53 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 (%)
25.0 Lower values reduce human off-target concern.
Human E-value
1.9e-09
Gut microbiome similarity
2.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
64.509 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
87.17 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 0.989
Structure A0A0H3GL69
Pocket Pocket 2
P2Rank 0.985
Structure A0A0H3GL69
Pocket Pocket 1
ColabFold model
FPocket 0.958 · Pocket 1
P2Rank 0.986 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 137 / 4744 genomes with a hit
Prevalence 2.9%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MAINPPAHNAAQAGRPRLRKSLKLWQVVMMGLAYLTPMTVFDTFGIVSGISNGHVPASYLLALAGVLFTAISYGKLVRQFPEAGSAYTYAQKSISPHVGFMVGWSSLLDYLFLPMINVLLAKIYLSALFPEVPPWVWVVTFVAILTAANLKSVNLVANFNTLFVLVQISIMVVFVILVVQGLHKGEGVGTVWSLQPFISQNAHLIPIITGATIVCFSFLGFDAVTTLSEETPDAARVIPKAIFLTAMYGGIIFIVASFFMQLFFPDIHRFKDPDAALPEIALYVGGKLFQSIFLCTTFVNTLASGLASHASVSRLLYVMGRDNVFPERIFGYVHPKWRTPALNVIMVGIVALSALFFDLVTATALINFGALVAFTFVNLSVFNHFWRRKGYNKTWKDRLHYLLLPMVGALTVGVLWINLEATSLTLGLVWAALGLLYLTYLTRRFRKPPPQFDAAKAEQAWES

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: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:0015489 Enables the transfer of putrescine from one side of a membrane to the other. Putrescine is 1,4-diaminobutane, the polyamine formed by decarboxylation of ornithine and the metabolic precursor of spermidine and spermine.
  • GO:0015295 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: solute(out) + H+(out) = solute(in) + H+(in).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
17 454 PANTHER PTHR42770 AMINO ACID TRANSPORTER-RELATED
418 422 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
242 264 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
340 359 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
365 386 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
222 240 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
290 312 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 23 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
18 449 FunFam G3DSA:1.20.1740.10:FF:000007 APC family permease
27 429 Pfam PF00324 Amino acid permease
27 429 InterPro IPR004841 Amino acid permease/ SLC12A domain
360 364 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
364 386 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
423 441 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
98 120 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
399 417 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
202 221 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
265 290 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
151 161 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
132 150 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
55 77 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
98 120 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
135 157 TMHMM TMhelix 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.
442 463 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
422 441 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
320 339 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
291 319 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
183 201 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
21 40 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
202 221 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
162 182 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
7 461 PIRSF PIRSF006060 AA_transporter
387 397 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
24 47 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
78 97 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
341 360 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
48 58 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
241 264 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
18 450 Gene3D G3DSA:1.20.1740.10 Amino acid/polyamine transporter I
398 417 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
162 182 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
59 77 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.

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
0.989
Likely same site as P2Rank 1 0.7 Å 44 shared residues 96% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #14
0.634
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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
0.985
Likely same site as FPocket 2 0.7 Å 44 shared residues 96% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.336
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Surrounding area
Site 3 P2Rank #3
0.246
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Surrounding area
Site 4 P2Rank #4
0.064
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Surrounding area
Site 5 P2Rank #5
0.024
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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_A0A0H3GL69
AlphaFold DB full sequence Viewing
ColabFold KP13_03903
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CLR PDB via homolog 386.7 Da · LogP 7.39 · TPSA 20.2 Open detail RCSB PDB
D10 PDB via homolog Detail RCSB PDB
OLC PDB via homolog Detail RCSB PDB
ZINC1501016272 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC1501016273 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
CLR RCSB PDB Q5L1G5 386.7 Da LogP 7.39 TPSA 20.2 1 viol. ✓ Clean CC(C)CCC[C@@H](C)[C@H]1CC[C@@H]2[C@@]1(CC[C@H]3…
D10 RCSB PDB Q58026 142.3 Da LogP 4.15 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCCCC
OLC RCSB PDB Q5L1G5 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)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.