Protein target profile

PA0206

spermidine/putrescine ABC transporter ATP-binding protein

Genome: NC_002516.2

Gene: PA0206 potA1 3D evidence: AlphaFold DB model UniProt Q9I6T2
Length 370
Pocket druggability 0.73
Ligand records 56
EC / GO 1 / 10
Target summary

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

4 signals
How to read 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 TPW 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.

Overview

Basic information about this protein and its source genome.

Accession
PA0206
Gene
PA0206 potA1
Status
annotated
Amino acids
370
3D evidence
AlphaFold DB model

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
36.471
Human E-value
3.52e-07
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
CytoplasmicMembrane

Selected pocket evidence

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 0.73
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MSALHSLRTHAVSIRAVRKVYGDPESGPVALKRVDLDIRDNEFFTLLGPSGCGKTTLLRMIAGFEFPTEGEILLYGENIAARPPFERPVNTVFQHYALFPHMSIAENLAFGLESRPLGRSLGKAEIAERVREMLALVQMERFADRRPGQLSGGQQQRVALARALAPQPRVLLLDEPLSALDLKLRQAMREELKAIQAKTGITFIFVTHDQEEALTMSDRIAVLSEGQVQQVGPPEEIYERPGNRFVADFIGETNFIEAELLQRDGPLALYRGPGGEAFEAAARDGLAAGARVCLSIRPERLDLLAANTGGGLPCTVESQVYLGTDLQYRVRLADGSLLTVRTPNGTARRFATGEAACLAVAKDSASVLLD

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
  • 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:0015417 Catalysis of the reaction: ATP + H2O + polyamine(out) = ADP + phosphate + polyamine(in).
  • GO:0140359 Primary active transporter characterized by two nucleotide-binding domains and two transmembrane domains. Uses the energy generated from ATP hydrolysis to drive the transport of a substance across a membrane.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0015847 The directed movement of putrescine into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Putrescine is 1,4-diaminobutane, the polyamine formed by decarboxylation of ornithine and the metabolic precursor of spermidine and spermine.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • 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:0015846 The directed movement of polyamines, organic compounds containing two or more amino groups, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
252 366 SUPERFAMILY SSF50331 MOP-like
252 366 InterPro IPR008995 Molybdate/tungstate binding, C-terminal
9 237 FunFam G3DSA:3.40.50.300:FF:000133 Spermidine/putrescine import ATP-binding protein PotA
10 360 PANTHER PTHR42781 SPERMIDINE/PUTRESCINE IMPORT ATP-BINDING PROTEIN POTA
40 226 SMART SM00382 AAA_5
40 226 InterPro IPR003593 AAA+ ATPase domain
46 342 NCBIfam TIGR01187 polyamine ABC transporter ATP-binding protein
46 342 InterPro IPR005893 Spermidine/putrescine import ATP-binding protein PotA-like
12 259 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
12 259 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
31 177 Pfam PF00005 ABC transporter
31 177 InterPro IPR003439 ABC transporter-like, ATP-binding domain
294 368 Pfam PF08402 TOBE domain
294 368 InterPro IPR013611 Transport-associated OB, type 2
11 237 Gene3D G3DSA:3.40.50.300 -
11 237 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
12 250 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
12 250 InterPro IPR003439 ABC transporter-like, ATP-binding domain
238 324 Gene3D G3DSA:2.40.50.100 -
150 164 ProSitePatterns PS00211 ABC transporters family signature.
150 164 InterPro IPR017871 ABC transporter-like, conserved site

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.

3D visualization script Full viewer

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Structural evidence

0 + 1

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 PA0206
AlphaFold DB full sequence Viewing
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
2 0.68
12 0.503

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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 56 via homologs
Structural ligands 6 0 loaded crystals
Bioactive compounds 0 50 ZINC proposed compounds
Drug-like & clean 33 0 PAINS alerts
Best available ligand signal
2BA PDB via homolog 658.4 Da · LogP -1.63 · TPSA 309.7 Open detail RCSB PDB
Detail RCSB PDB 2BA PDB via homolog
Detail RCSB PDB AGS PDB via homolog
Detail RCSB PDB ANP PDB via homolog
Detail RCSB PDB BET PDB via homolog

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
2BA RCSB PDB Q9KIF7 658.4 Da LogP -1.63 TPSA 309.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)C…
AGS RCSB PDB P30750 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB Q97UY8 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BET RCSB PDB Q9KIF7 118.2 Da LogP -0.22 TPSA 37.3 ✓ Ro5 ✓ Clean C[N+](C)(C)CC(=O)O
NH4 RCSB PDB Q9YGA6 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
POP RCSB PDB O57933 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[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.