Protein profile

PA4628

lysine-specific permease

Genome: NC_002516.2

Gene: PA4628 lysP Structure source: AlphaFold UniProt Q9HVG3

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Amino acids 487

Annotations 5

Features 45

PDB binders 3

Druggability 0.825

Overview

Basic information about this protein and its source genome.

Accession: PA4628
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4628 lysP
Status: annotated
Amino acids: 487
Structure source: AlphaFold

GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it. GO:0015171 Enables the transfer of amino acids from one side of a membrane to the other. Amino acids are organic molecules that contain an amino group and a carboxyl group. GO:0003333 The process in which an amino acid is transported across a membrane. GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GO:0006865 The directed movement of amino acids, organic acids containing one or more amino substituents, 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: hit
Human identity (%): 24.932
Human E-value: 2.6e-11
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: CytoplasmicMembrane

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 0.825

Structure –

Pocket –

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:0015171 Enables the transfer of amino acids from one side of a membrane to the other. Amino acids are organic molecules that contain an amino group and a carboxyl group.
GO:0003333 The process in which an amino acid is transported across a membrane.
GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
GO:0006865 The directed movement of amino acids, organic acids containing one or more amino substituents, 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.

45 records

Show feature table

Start	End	DB	Term	Name
48	65	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
244	263	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
244	266	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
66	101	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
125	129	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
446	466	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
129	151	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
130	147	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
20	476	Pfam	PF00324	Amino acid permease
20	476	InterPro	IPR004841	Amino acid permease/ SLC12A domain
7	484	PANTHER	PTHR43341	AMINO ACID PERMEASE
415	434	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
290	312	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
11	477	FunFam	G3DSA:1.20.1740.10:FF:000001	Amino acid permease
224	243	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
347	364	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
312	346	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
365	369	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
396	414	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
45	76	ProSitePatterns	PS00218	Amino acid permeases signature.
45	76	InterPro	IPR004840	Amino acid permease, conserved site
467	487	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
201	223	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
21	42	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
148	158	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
11	480	Gene3D	G3DSA:1.20.1740.10	Amino acid/polyamine transporter I
368	390	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
370	395	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
415	434	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
290	311	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
102	124	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
159	181	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
444	466	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	20	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
158	180	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
102	124	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
21	43	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
182	200	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
264	289	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
43	47	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
435	445	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
342	364	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
2	484	PIRSF	PIRSF006060	AA_transporter
195	217	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
48	65	TMHMM	TMhelix	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.

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Structural evidence

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA4628	AlphaFold	—	—	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
6				0.825
7				0.275
12				0.241
17				0.227

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.

67 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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL1417204	P25376	6.52	251.2 Da LogP 2.83 TPSA 60.2	✓ Ro5	✓ Clean	`O=C(C#Cc1cccc([N+](=O)[O-])c1)c1ccccc1`
CHEMBL1425137	P25376	6.24	253.7 Da LogP 2.85 TPSA 46.2	✓ Ro5	✓ Clean	`CC(C)(C)C(=O)C(Cl)C(=O)Nc1ccccc1`
CHEMBL1492648	P25376	6.18	302.3 Da LogP 2.57 TPSA 59.9	✓ Ro5	✓ Clean	`CS(=O)(=O)c1nc(-c2ccccc2)cc(C(F)(F)F)n1`
CHEMBL1584597	P25376	6.11	301.8 Da LogP 3.73 TPSA 46.2	✓ Ro5	✓ Clean	`Cc1cccc(C)c1NC(=O)C(Cl)C(=O)c1ccccc1`
CHEMBL3199814	P25376	6.08	367.5 Da LogP 4.92 TPSA 46.5	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)/N=C(\Sc2ccccc2)c2ccccc2)cc1`
CHEMBL1430895	P25376	6.06	308.3 Da LogP 2.63 TPSA 59.9	✓ Ro5	✓ Clean	`CS(=O)(=O)c1nc(-c2cccs2)cc(C(F)(F)F)n1`
CHEMBL1370681	P25376	6.03	374.3 Da LogP 2.50 TPSA 86.2	✓ Ro5	✓ Clean	`COC(=O)CCS(=O)(=O)c1nc(-c2ccccc2)cc(C(F)(F)F)n1`
CHEMBL1429929	P25376	6.03	388.4 Da LogP 2.89 TPSA 86.2	✓ Ro5	✓ Clean	`CCOC(=O)CCS(=O)(=O)c1nc(-c2ccccc2)cc(C(F)(F)F)n1`
CHEMBL11298	P19145	—	105.1 Da LogP -1.61 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](CO)C(=O)O`
CHEMBL1221825	P19145	—	468.6 Da LogP 0.12 TPSA 183.4	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](N)C(=O)N[C@@H](Cc1ccccc1)C(=O)N…`
CHEMBL1221826	P19145	—	294.3 Da LogP 0.51 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@@H](CC(=O)N[C@@H](CCC(=O)O)c1ccccc1)C(=O)O`
CHEMBL55711	P19145	—	188.2 Da LogP -0.44 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)NCC(=O)O`
CIR	P19145	—	175.2 Da LogP -1.15 TPSA 118.4	✓ Ro5	✓ Clean	`C(C[C@@H](C(=O)O)N)CNC(=O)N`
GGL	P19145	—	147.1 Da LogP -0.74 TPSA 100.6	✓ Ro5	✓ Clean	`C(CC(=O)O)[C@@H](C(=O)O)N`

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`
ZINC215164	1.000	302.3 Da LogP 2.57 TPSA 59.9	✓ Ro5	✓ Clean	`CS(=O)(=O)c1nc(-c2ccccc2)cc(C(F)(F)F)n1`
ZINC221534416	1.000	328.5 Da LogP 4.14 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCC(=O)OC[C@@H](O)CO`
ZINC2439648	1.000	374.3 Da LogP 2.50 TPSA 86.2	✓ Ro5	✓ Clean	`COC(=O)CCS(=O)(=O)c1nc(-c2ccccc2)cc(C(F)(F)F)n1`
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`
ZINC984397	1.000	251.2 Da LogP 2.83 TPSA 60.2	✓ Ro5	✓ Clean	`O=C(C#Cc1cccc([N+](=O)[O-])c1)c1ccccc1`
ZINC2384822	0.953	321.4 Da LogP -0.61 TPSA 154.3	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](N)C(=O)N[C@@H](Cc1ccccc1)C(=O)O`
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`
ZINC1575521	0.862	245.3 Da LogP -1.32 TPSA 121.5	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)NCC(=O)NCC(=O)O`
ZINC1708209	0.862	245.3 Da LogP -1.32 TPSA 121.5	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)NCC(=O)NCC(=O)O`
ZINC275255	0.833	251.2 Da LogP 2.83 TPSA 60.2	✓ Ro5	✓ Clean	`O=C(C#Cc1ccccc1)c1cccc([N+](=O)[O-])c1`
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`
ZINC2516269	0.824	246.3 Da LogP 2.02 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCCCC(=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`
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`

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.