Protein profile

PA0301

spermidine ABC transporter substrate-binding protein SpuE

Genome: NC_002516.2

Gene: spuE PA0301 Structure source: Experimental + AlphaFold UniProt Q9I6J0

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Amino acids 365

Annotations 8

Features 36

PDB binders 11

Druggability 0.599

Overview

Basic information about this protein and its source genome.

Accession: PA0301
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: spuE PA0301
Status: annotated
Amino acids: 365
Structure source: Experimental + AlphaFold

GO:0005615 OBSOLETE. That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid. 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: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: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.

Target profile

Computed evidence for target prioritization.

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

Selected Druggability evidence

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.599

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

MQHSIGKTLLVAALATAIAGPVQAEKKSLHIYNWTDYIAPTTLKDFTKESGIDVSYDVFDSNETLEGKLVSGHSGYDIVVPSNNFLGKQIQAGAFQKLDKSKLPNWKNLDPALLKQLEVSDPGNQYAVPYLWGTNGIGYNVAKVKEVLGDQPIDSWAILFEPENMKKLAKCGVAFMDSGDEMLPAALNYLGLDPNTHDPKDYKKAEEVLTKVRPYVSYFHSSKYISDLANGNICVAFGYSGDVFQAAARAEEAGKGIDIQYVIPKEGANLWFDLMAIPADAKAADNAYAFIDYLLRPEVIAKVSDYVGYANAIPGARPLMDKSVSDSEEVYPPQAVLDKLYVSAVLPAKVLRLQTRTWTRIKTGK

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

GO:0005615 OBSOLETE. That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
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: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: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:0019808 Binding to a polyamine, an organic compound containing two or more amino groups.

Sequence Features

Domain/signature hits from InterPro and related databases.

36 records

Show feature table

Start	End	DB	Term	Name
1	7	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	24	SignalP_EUK	SignalP-noTM	SignalP-noTM
20	24	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	365	PIRSF	PIRSF019574	Periplasmic_polyamine_BP
1	365	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
133	360	Gene3D	G3DSA:3.40.190.10	-
29	358	CDD	cd13659	PBP2_PotF
29	331	Gene3D	G3DSA:3.40.190.10	-
1	24	Phobius	SIGNAL_PEPTIDE	Signal peptide region
1	24	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
27	364	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
75	89	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
75	89	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
214	233	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
214	233	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
154	168	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
154	168	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
32	48	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
32	48	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
48	69	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
48	69	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
309	335	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
309	335	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
124	140	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
124	140	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
177	196	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
177	196	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
91	104	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
91	104	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
264	283	PRINTS	PR00909	Bacterial periplasmic spermidine/putrescine-binding protein signature
264	283	InterPro	IPR001188	Spermidine/putrescine-binding periplasmic protein
14	361	PANTHER	PTHR30222	SPERMIDINE/PUTRESCINE-BINDING PERIPLASMIC PROTEIN
8	19	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
25	365	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
43	324	Pfam	PF13416	Bacterial extracellular solute-binding protein
43	324	InterPro	IPR006059	Bacterial extracellular solute-binding protein

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

3 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 3TTN	X-ray	2.00 Å	A,B	91.8% 28-362	PDBe RCSB PDBj File	Viewing
PDB 3TTL	X-ray	2.30 Å	A,B	91.8% 28-362	PDBe RCSB PDBj File	Loaded
PDB 6IKM	X-ray	3.40 Å	A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R	91.8% 28-362	PDBe RCSB PDBj File	Loaded
AlphaFold PA0301	AlphaFold	—	—	full sequence	—	Loaded

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
1				0.599
10				0.298

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	12.36	0.648
2	6.5	0.329
3	5.21	0.242
4	3.09	0.104
5	0.65	0.001

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
1				0.585
5				0.244

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.

61 records

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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
SPD	3TTN 2.00 Å Open crystal	145.2 Da LogP -0.34 TPSA 64.1	✓ Ro5	✓ Clean	`C(CCNCCCN)CN`

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
AG2	6YE6	P31133	130.2 Da LogP -0.79 TPSA 87.9	✓ Ro5	✓ Clean	`C(CCNC(=N)N)CN`
JFN	6YE0	P31133	89.1 Da LogP -0.02 TPSA 35.2	✓ Ro5	✓ Clean	`C[C@H](COC)N`
MLI	6YE7	P31133	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=O)[O-]`
N2P	6YE7	P31133	102.2 Da LogP 0.07 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CCN`
ONT	6YE0	P31133	133.2 Da LogP -0.00 TPSA 44.5	✓ Ro5	✓ Clean	`C[C@@H](COCCOC)N`
ONW	6YE0	P31133	191.3 Da LogP 0.40 TPSA 53.7	✓ Ro5	✓ Clean	`C[C@H](CO[C@H](C)COCCOC)N`
P33	6YE7	P31133	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`C(COCCOCCOCCOCCOCCOCCO)O`
PUT	1A99	P31133	88.2 Da LogP -0.32 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CN`
SPM	6YEC	P31133	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`C(CCNCCCN)CNCCCN`
TAM	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	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC27564039	0.933	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCNCCCN`
ZINC13377742	0.929	230.4 Da LogP 0.42 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCCNCCCCN`
ZINC1532734	0.929	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCNCCCCNCCCN`
ZINC1598087	0.867	215.4 Da LogP 1.61 TPSA 64.1	✓ Ro5	✓ Clean	`NCCCCCCNCCCCCCN`
ZINC13545924	0.737	214.3 Da LogP -0.10 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCCNC(=N)N`
ZINC1561855	0.737	200.3 Da LogP -0.49 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCNC(=N)N`
ZINC2013578	0.737	228.3 Da LogP 0.29 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCCCNC(=N)N`
ZINC3995661	0.737	256.4 Da LogP 1.07 TPSA 123.8	1 viol.	✓ Clean	`N=C(N)NCCCCCCCCCCNC(=N)N`
ZINC115086873	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC100056474	0.650	270.5 Da LogP 4.63 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCNCCCN`
ZINC107767463	0.650	200.4 Da LogP 2.68 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCNCCCCCCN`
ZINC59496006	0.650	242.5 Da LogP 3.85 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNCCCN`
ZINC144169243	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC575441396	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC2575038	0.625	205.3 Da LogP 0.00 TPSA 86.7	✓ Ro5	✓ Clean	`NC(CCCO)(CCCO)CCCO`
ZINC1644613	0.611	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC258839852	0.611	276.3 Da LogP 0.61 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCC(F)(F)F`
ZINC167715346	0.600	266.3 Da LogP -0.18 TPSA 77.4	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCOCCCO`
ZINC34160867	0.600	222.3 Da LogP -0.20 TPSA 68.2	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCCO`
ZINC1580159	0.588	210.3 Da LogP -0.26 TPSA 58.9	✓ Ro5	✓ Clean	`OCCOCCSCCOCCO`
ZINC1666747	0.583	227.4 Da LogP 3.39 TPSA 61.9	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNC(=N)N`
ZINC575440725	0.579	295.4 Da LogP -1.03 TPSA 80.6	✓ Ro5	✓ Clean	`CN(CCOCCOCCO)CCOCCOCCO`

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.