Protein target profile

PA0295

polyamine binding protein

Genome: NC_002516.2

Gene: PA0295 3D evidence: AlphaFold DB model UniProt Q9I6J6

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Length 353

Pocket druggability 0.712

Ligand records 62

EC / GO 0 / 7

Target summary

Promising target candidate with multiple supporting evidence streams.

5 signals

Strengths

Risks / watch

No major risk signal surfaced in the loaded evidence.

Missing evidence

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.

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: PA0295
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA0295
Status: annotated
Amino acids: 353
3D evidence: AlphaFold DB model

GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall. GO:0019810 Binding to putrescine, 1,4-diaminobutane, the polyamine formed by decarboxylation of ornithine and the metabolic precursor of spermidine and spermine. GO:0019809 Binding to spermidine, N-(3-aminopropyl)-1,4-diaminobutane. 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:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria). 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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: Hit
Essential (DEG): N
Localization: Periplasmic

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 0.712

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MPRLSALLFLALAPWLAQAEETLRVYNWNDYIDPQVLESFQKDTGIRVEYHTFATAEELDKALRSGEAIDVAVPSHDTLPALLKDNLLRPLDFTQLPNRSHLDRQLLSKLAAVDPDNRHAVPYLWGAVGLAINTPQAEAAYGGPLPNSWSLLFDASQSQRLKSCGISLLDAPDETLAILLNYQGRNLGRTAPSQVRRAAEALHGLRPNLRYVDSERYIADLEGGRLCLAMAWVGDALRAAKAGQPVSFEVPQEGSVLFIDNLVIPAGAQHPREAHRFIDYLMQPKIAAQITAATLYPSGNADAAGFLDPALRQQPGLYPDRDTSRRLFALETPPEKLRPVVDEIWKAFRGASH

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
GO:0019810 Binding to putrescine, 1,4-diaminobutane, the polyamine formed by decarboxylation of ornithine and the metabolic precursor of spermidine and spermine.
GO:0019809 Binding to spermidine, N-(3-aminopropyl)-1,4-diaminobutane.
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:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
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.
GO:0019808 Binding to a polyamine, an organic compound containing two or more amino groups.

Sequence Features

Domain/signature hits from InterPro and related databases.

34 records

Show feature table

Start	End	DB	Term	Name
26	42	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
4	12	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
36	310	Pfam	PF13416	Bacterial extracellular solute-binding protein
36	310	InterPro	IPR006059	Bacterial extracellular solute-binding protein
1	19	Phobius	SIGNAL_PEPTIDE	Signal peptide region
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	19	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM
20	353	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
117	133	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
117	133	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
42	63	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
42	63	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
84	97	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
84	97	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
147	161	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
147	161	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
170	189	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
170	189	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
296	322	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
296	322	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
207	226	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
207	226	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
251	270	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
251	270	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
26	42	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
22	345	CDD	cd13659	PBP2_PotF
13	19	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
126	346	Gene3D	G3DSA:3.40.190.10	-
23	318	Gene3D	G3DSA:3.40.190.10	-
1	19	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
20	348	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
4	352	PIRSF	PIRSF019574	Periplasmic_polyamine_BP
4	352	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
17	348	PANTHER	PTHR30222	SPERMIDINE/PUTRESCINE-BINDING PERIPLASMIC PROTEIN

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.

Loading 3D structure...

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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 PA0295	AlphaFold DB	—	—	full sequence	—	Viewing

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

0.712

Show in viewer

Site 2 FPocket #12

0.224

Show in viewer

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.

62 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 62 via homologs

Structural ligands 12 0 loaded crystals

Bioactive compounds 0 50 ZINC proposed compounds

Drug-like & clean 53 0 PAINS alerts

Best available ligand signal

ABU PDB via homolog 103.1 Da · LogP -0.19 · TPSA 63.3 Open detail RCSB PDB

Detail RCSB PDB ABU PDB via homolog

Detail RCSB PDB AG2 PDB via homolog

Detail RCSB PDB JFN PDB via homolog

Detail RCSB PDB MLI PDB via homolog

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ABU RCSB PDB	4EUO	A9CGA5	103.1 Da LogP -0.19 TPSA 63.3	✓ Ro5	✓ Clean	`C(CC(=O)O)CN`
AG2 RCSB PDB	6YE6	P31133	130.2 Da LogP -0.79 TPSA 87.9	✓ Ro5	✓ Clean	`C(CCNC(=N)N)CN`
JFN RCSB PDB	6YE0	P31133	89.1 Da LogP -0.02 TPSA 35.2	✓ Ro5	✓ Clean	`C[C@H](COC)N`
MLI RCSB PDB	6YE7	P31133	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
N2P RCSB PDB	6YE7	P31133	102.2 Da LogP 0.07 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CCN`
ONT RCSB PDB	6YE0	P31133	133.2 Da LogP -0.00 TPSA 44.5	✓ Ro5	✓ Clean	`C[C@@H](COCCOC)N`
ONW RCSB PDB	6YE0	P31133	191.3 Da LogP 0.40 TPSA 53.7	✓ Ro5	✓ Clean	`C[C@H](CO[C@H](C)COCCOC)N`
P33 RCSB PDB	6YE7	P31133	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`C(COCCOCCOCCOCCOCCOCCO)O`
PUT RCSB PDB	1A99	P31133	88.2 Da LogP -0.32 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CN`
SPD RCSB PDB	1POT	P0AFK9	145.2 Da LogP -0.34 TPSA 64.1	✓ Ro5	✓ Clean	`C(CCNCCCN)CN`
SPM RCSB PDB	6YEC	P31133	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`C(CCNCCCN)CNCCCN`
TAM RCSB PDB	6YE7	P31133	163.2 Da LogP -1.17 TPSA 86.7	✓ Ro5	✓ Clean	`C(CO)C(CCO)(CCO)N`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC12501520 ZINC	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716 ZINC	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769 ZINC	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548 ZINC	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829 ZINC	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830 ZINC	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC27564039 ZINC	0.933	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCNCCCN`
ZINC13377742 ZINC	0.929	230.4 Da LogP 0.42 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCCNCCCCN`
ZINC1532734 ZINC	0.929	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCNCCCCNCCCN`
ZINC1598087 ZINC	0.867	215.4 Da LogP 1.61 TPSA 64.1	✓ Ro5	✓ Clean	`NCCCCCCNCCCCCCN`
ZINC13357569 ZINC	0.778	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCC(=O)O`
ZINC13545924 ZINC	0.737	214.3 Da LogP -0.10 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCCNC(=N)N`
ZINC1561855 ZINC	0.737	200.3 Da LogP -0.49 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCNC(=N)N`
ZINC2013578 ZINC	0.737	228.3 Da LogP 0.29 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCCCNC(=N)N`
ZINC3995661 ZINC	0.737	256.4 Da LogP 1.07 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCCCCCNC(=N)N`
ZINC115086873 ZINC	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264 ZINC	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823 ZINC	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442 ZINC	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710 ZINC	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161 ZINC	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118 ZINC	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257 ZINC	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028 ZINC	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057 ZINC	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776 ZINC	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654 ZINC	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157 ZINC	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059 ZINC	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101 ZINC	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743 ZINC	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860 ZINC	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917 ZINC	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182 ZINC	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921 ZINC	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446 ZINC	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447 ZINC	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC100056474 ZINC	0.650	270.5 Da LogP 4.63 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCNCCCN`
ZINC107767463 ZINC	0.650	200.4 Da LogP 2.68 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCNCCCCCCN`
ZINC59496006 ZINC	0.650	242.5 Da LogP 3.85 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNCCCN`
ZINC144169243 ZINC	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716 ZINC	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC575441396 ZINC	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC2575038 ZINC	0.625	205.3 Da LogP 0.00 TPSA 86.7	✓ Ro5	✓ Clean	`NC(CCCO)(CCCO)CCCO`
ZINC1644613 ZINC	0.611	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC258839852 ZINC	0.611	276.3 Da LogP 0.61 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCC(F)(F)F`
ZINC167715346 ZINC	0.600	266.3 Da LogP -0.18 TPSA 77.4	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCOCCCO`
ZINC34160867 ZINC	0.600	222.3 Da LogP -0.20 TPSA 68.2	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCCO`
ZINC3860440 ZINC	0.588	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298 ZINC	0.588	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=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.