Protein profile

KP13_03903

Putrescine importer

Genome: KpKP13

Gene: AHE45351.1 puuP Structure source: AlphaFold + ColabFold UniProt A0A0H3GL69

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Amino acids 463

Annotations 5

Features 43

PDB binders 3

Druggability 0.989

Overview

Basic information about this protein and its source genome.

Accession: KP13_03903
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45351.1 puuP
Status: annotated
Amino acids: 463
Structure source: AlphaFold + ColabFold

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).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 25.0
Human E-value: 1.9e-09
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 64.509
DEG E-value: 0.0
Localization: CytoplasmicMembrane
ColabFold pLDDT: 87.17

Selected Druggability evidence

AlphaFold / UniProt model

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 0.989

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

Normalized 0.029

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GL69	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03903	ColabFold	—	—	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
2				0.989
14				0.634

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	40.92	0.965
2	6.48	0.328
3	5.96	0.292
4	2.83	0.088
5	2.13	0.049

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				0.958
14				0.356

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	41.93	0.967
2	7.96	0.423
3	6.53	0.33
4	3.19	0.109
5	2.63	0.077

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

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
CLR	5OQT	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	3GIA	Q58026	142.3 Da LogP 4.15 TPSA 0.0	✓ Ro5	✓ Clean	`CCCCCCCCCC`
OLC	5OQT	Q5L1G5	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)O`

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
ZINC1501016272	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCC/C=C\CCCCCCC(=O)OC[C@H](O)CO`
ZINC1501016273	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCC/C=C\CCCCCCC(=O)OC[C@@H](O)CO`
ZINC1501016315	1.000	314.5 Da LogP 3.75 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCC(=O)OC[C@@H](O)CO`
ZINC1501016316	1.000	314.5 Da LogP 3.75 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCC(=O)OC[C@H](O)CO`
ZINC2038077522	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCC=CCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC2038077523	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCC=CCCCCCCCC(=O)OC[C@H](O)CO`
ZINC221534416	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCC(=O)OC[C@@H](O)CO`
ZINC32840893	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840894	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C/CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840895	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840896	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840901	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840902	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840903	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840904	1.000	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC725433050	1.000	342.5 Da LogP 4.53 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCC(=O)OC[C@@H](O)CO`
ZINC725433052	1.000	342.5 Da LogP 4.53 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCC(=O)OC[C@H](O)CO`
ZINC98208566	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCC(=O)OC[C@H](O)CO`
ZINC32840885	0.943	300.4 Da LogP 3.36 TPSA 66.8	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC2053467566	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC=CCC=CCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC2053467567	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCC=CCC=CCCCCCCCC(=O)OC[C@H](O)CO`
ZINC29045599	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC4557100	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC4557101	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC5819989	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC5819990	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C/C/C=C/CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC85425978	0.919	354.5 Da LogP 4.70 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC29045446	0.892	352.5 Da LogP 4.47 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCC/C=C\C/C=C\C/C=C\CCCCC(=O)OC[C@@H](O)CO`
ZINC13532428	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)C/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC13532431	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)C/C=C/CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC13532435	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)C/C=C\CCCCCCCC(=O)OC[C@@H](O)CO`
ZINC13546140	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)C/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC13546141	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)C/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC2296552808	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)CC=CCCCCCCCC(=O)OC[C@H](O)CO`
ZINC2296552809	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)CC=CCCCCCCCC(=O)OC[C@H](O)CO`
ZINC33832849	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)C/C=C\CCCCCCCC(=O)OC[C@H](O)CO`
ZINC35052109	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)C/C=C/CCCCCCCC(=O)OC[C@H](O)CO`
ZINC4411072	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@H](O)CC=CCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC4411074	0.829	372.5 Da LogP 3.89 TPSA 87.0	✓ Ro5	✓ Clean	`CCCCCC[C@@H](O)CC=CCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC100297583	0.824	232.3 Da LogP 1.63 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC100503477	0.824	260.4 Da LogP 2.41 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCCC(=O)OC[C@H](O)CO`
ZINC2516268	0.824	218.3 Da LogP 1.24 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@H](O)CO`
ZINC2516269	0.824	246.3 Da LogP 2.02 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OC[C@H](O)CO`
ZINC2568190	0.824	232.3 Da LogP 1.63 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840883	0.824	302.5 Da LogP 3.58 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840884	0.824	302.5 Da LogP 3.58 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(=O)OC[C@H](O)CO`
ZINC32840889	0.824	316.5 Da LogP 3.97 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC32840890	0.824	316.5 Da LogP 3.97 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(=O)OC[C@H](O)CO`
ZINC38153421	0.824	246.3 Da LogP 2.02 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCC(=O)OC[C@@H](O)CO`
ZINC8674155	0.824	218.3 Da LogP 1.24 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC(=O)OC[C@@H](O)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.