Protein profile

PA0438

cytosine permease

Genome: NC_002516.2

Gene: PA0438 codB Structure source: AlphaFold UniProt Q9I679

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Amino acids 416

Annotations 6

Features 43

PDB binders 5

Druggability 0.919

Overview

Basic information about this protein and its source genome.

Accession: PA0438
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA0438 codB
Status: annotated
Amino acids: 416
Structure source: AlphaFold

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:0015209 Enables the transfer of cytosine, 4-amino-2-hydroxypyrimidine from one side of a membrane to the other. GO:0019858 The chemical reactions and pathways involving cytosine, 4-amino-2-hydroxypyrimidine, a pyrimidine derivative that is one of the five main bases found in nucleic acids; it occurs widely in cytidine derivatives. 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:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other. GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
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 0.919

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

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:0015209 Enables the transfer of cytosine, 4-amino-2-hydroxypyrimidine from one side of a membrane to the other.
GO:0019858 The chemical reactions and pathways involving cytosine, 4-amino-2-hydroxypyrimidine, a pyrimidine derivative that is one of the five main bases found in nucleic acids; it occurs widely in cytidine derivatives.
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:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.

Sequence Features

Domain/signature hits from InterPro and related databases.

43 records

Show feature table

Start	End	DB	Term	Name
11	397	Pfam	PF02133	Permease for cytosine/purines, uracil, thiamine, allantoin
11	397	InterPro	IPR001248	Purine-cytosine permease
1	19	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
149	154	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
12	404	CDD	cd11484	SLC-NCS1sbd_CobB-like
356	375	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
119	129	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
284	306	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
193	212	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
20	40	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
319	323	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
2	416	FunFam	G3DSA:1.10.4160.10:FF:000003	Cytosine permease
75	94	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
381	398	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
255	277	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
376	380	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
297	318	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
95	118	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
321	340	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
213	223	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
41	51	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
324	344	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
278	296	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
130	148	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
223	245	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
96	118	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
259	277	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
152	174	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
2	412	Gene3D	G3DSA:1.10.4160.10	Hydantoin permease
128	150	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
155	173	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
52	74	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
399	416	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
224	247	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
189	211	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
360	382	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
2	413	PANTHER	PTHR30569	CYTOSINE TRANSPORTER CODB
2	413	InterPro	IPR030191	Cytosine permease
21	43	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
174	192	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
53	75	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
248	258	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
345	355	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.

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 PA0438	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
1				0.753
6				0.476

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.

55 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
5FH	4D1B	D6R8X8	190.2 Da LogP 0.44 TPSA 58.2	✓ Ro5	✓ Clean	`c1ccc(cc1)C[C@H]2C(=O)NC(=O)N2`
5ND	4D1D	D6R8X8	240.3 Da LogP 1.59 TPSA 58.2	✓ Ro5	✓ Clean	`c1ccc2cc(ccc2c1)C[C@@H]3C(=O)NC(=O)N3`
5NL	4D1D	D6R8X8	240.3 Da LogP 1.59 TPSA 58.2	✓ Ro5	✓ Clean	`c1ccc2cc(ccc2c1)C[C@H]3C(=O)NC(=O)N3`
B5H	4D1C	D6R8X8	267.1 Da LogP 1.63 TPSA 58.2	✓ Ro5	✓ Clean	`c1cc(cc(c1)Br)/C=C\2/C(=O)NC(=O)N2`
I5H	4D1A	D6R8X8	229.2 Da LogP 0.92 TPSA 74.0	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(c[nH]2)C[C@H]3C(=O)NC(=O)N3`

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
ZINC1093415	1.000	267.1 Da LogP 1.63 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1NC(=O)/C(=C\c2cccc(Br)c2)N1`
ZINC16386114	1.000	267.1 Da LogP 1.63 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1NC(=O)/C(=C/c2cccc(Br)c2)N1`
ZINC1682922	1.000	229.2 Da LogP 0.92 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](Cc2c[nH]c3ccccc23)N1`
ZINC2043051	1.000	229.2 Da LogP 0.92 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](Cc2c[nH]c3ccccc23)N1`
ZINC18209074	0.800	372.4 Da LogP 2.42 TPSA 89.8	✓ Ro5	✓ Clean	`O=C1N[C@H](Cc2c[nH]c3ccccc23)C(=O)N[C@H]1Cc1c[n…`
ZINC2113938	0.800	372.4 Da LogP 2.42 TPSA 89.8	✓ Ro5	✓ Clean	`O=C1N[C@H](Cc2c[nH]c3ccccc23)C(=O)N[C@@H]1Cc1c[…`
ZINC4073922	0.800	372.4 Da LogP 2.42 TPSA 89.8	✓ Ro5	✓ Clean	`O=C1N[C@@H](Cc2c[nH]c3ccccc23)C(=O)N[C@H]1Cc1c[…`
ZINC28526335	0.750	245.3 Da LogP 1.08 TPSA 56.9	✓ Ro5	✓ Clean	`O=C1NC(=S)N[C@@H]1Cc1c[nH]c2ccccc12`
ZINC28526336	0.750	245.3 Da LogP 1.08 TPSA 56.9	✓ Ro5	✓ Clean	`O=C1NC(=S)N[C@H]1Cc1c[nH]c2ccccc12`
ZINC18061788	0.741	294.4 Da LogP 1.45 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1N[C@H](Cc2ccccc2)C(=O)N[C@H]1Cc1ccccc1`
ZINC2038712	0.741	294.4 Da LogP 1.45 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1N[C@@H](Cc2ccccc2)C(=O)N[C@H]1Cc1ccccc1`
ZINC2038715	0.741	294.4 Da LogP 1.45 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1N[C@H](Cc2ccccc2)C(=O)N[C@@H]1Cc1ccccc1`
ZINC15773085	0.722	283.1 Da LogP 1.79 TPSA 41.1	✓ Ro5	✓ Clean	`O=C1NC(=S)N/C1=C\c1cccc(Br)c1`
ZINC1669933	0.710	224.6 Da LogP 1.09 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](Cc2ccc(Cl)cc2)N1`
ZINC2045152	0.710	224.6 Da LogP 1.09 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](Cc2ccc(Cl)cc2)N1`
ZINC5769509	0.710	208.2 Da LogP 0.58 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](Cc2ccc(F)cc2)N1`
ZINC5769537	0.710	208.2 Da LogP 0.58 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](Cc2ccc(F)cc2)N1`
ZINC13430262	0.700	273.3 Da LogP -0.31 TPSA 94.2	✓ Ro5	✓ Clean	`O=C1N[C@H](CO)C(=O)N[C@H]1Cc1c[nH]c2ccccc12`
ZINC13430264	0.700	273.3 Da LogP -0.31 TPSA 94.2	✓ Ro5	✓ Clean	`O=C1N[C@H](Cc2c[nH]c3ccccc23)C(=O)N[C@H]1CO`
ZINC13430265	0.700	273.3 Da LogP -0.31 TPSA 94.2	✓ Ro5	✓ Clean	`O=C1N[C@@H](Cc2c[nH]c3ccccc23)C(=O)N[C@H]1CO`
ZINC2560888	0.700	333.4 Da LogP 1.94 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1N[C@H](Cc2c[nH]c3ccccc23)C(=O)N[C@@H]1Cc1cc…`
ZINC4899716	0.700	333.4 Da LogP 1.94 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1N[C@@H](Cc2c[nH]c3ccccc23)C(=O)N[C@H]1Cc1cc…`
ZINC6096559	0.700	333.4 Da LogP 1.94 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1N[C@H](Cc2ccccc2)C(=O)N[C@H]1Cc1c[nH]c2cccc…`
ZINC6096622	0.700	333.4 Da LogP 1.94 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1N[C@H](Cc2c[nH]c3ccccc23)C(=O)N[C@H]1Cc1ccc…`
ZINC1754395	0.688	204.2 Da LogP 0.75 TPSA 58.2	✓ Ro5	✓ Clean	`Cc1ccc(C[C@H]2NC(=O)NC2=O)cc1`
ZINC2034264	0.688	204.2 Da LogP 0.75 TPSA 58.2	✓ Ro5	✓ Clean	`Cc1ccc(C[C@@H]2NC(=O)NC2=O)cc1`
ZINC3290147	0.688	204.2 Da LogP 0.83 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](CCc2ccccc2)N1`
ZINC3290149	0.688	204.2 Da LogP 0.83 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](CCc2ccccc2)N1`
ZINC410261	0.688	206.2 Da LogP 0.14 TPSA 78.4	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](Cc2ccc(O)cc2)N1`
ZINC410262	0.688	206.2 Da LogP 0.14 TPSA 78.4	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H](Cc2ccc(O)cc2)N1`
ZINC5589124	0.688	205.2 Da LogP 0.02 TPSA 84.2	✓ Ro5	Alert	`Nc1ccc(C[C@H]2NC(=O)NC2=O)cc1`
ZINC5589126	0.688	205.2 Da LogP 0.02 TPSA 84.2	✓ Ro5	Alert	`Nc1ccc(C[C@@H]2NC(=O)NC2=O)cc1`
ZINC6096554	0.688	206.3 Da LogP 0.60 TPSA 41.1	✓ Ro5	✓ Clean	`O=C1NC(=S)N[C@@H]1Cc1ccccc1`
ZINC6096619	0.688	206.3 Da LogP 0.60 TPSA 41.1	✓ Ro5	✓ Clean	`O=C1NC(=S)N[C@H]1Cc1ccccc1`
ZINC12341748	0.686	222.6 Da LogP 1.52 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1NC(=O)/C(=C\c2cccc(Cl)c2)N1`
ZINC13413571	0.683	257.3 Da LogP 0.71 TPSA 74.0	✓ Ro5	✓ Clean	`C[C@@H]1NC(=O)[C@H](Cc2c[nH]c3ccccc23)NC1=O`
ZINC247754165	0.674	300.4 Da LogP 0.43 TPSA 100.0	✓ Ro5	✓ Clean	`NCCC[C@@H]1NC(=O)[C@@H](Cc2c[nH]c3ccccc23)NC1=O`
ZINC34114304	0.674	245.2 Da LogP 0.62 TPSA 94.2	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H](Cc2c[nH]c3ccc(O)cc23)N1`
ZINC100662888	0.667	204.2 Da LogP 0.57 TPSA 78.4	✓ Ro5	✓ Clean	`O=C1NC(=O)/C(=C/c2cccc(O)c2)N1`
ZINC12410471	0.667	202.2 Da LogP 1.18 TPSA 58.2	✓ Ro5	✓ Clean	`Cc1cccc(/C=C2\NC(=O)NC2=O)c1`
ZINC13139308	0.667	204.2 Da LogP 0.57 TPSA 78.4	✓ Ro5	✓ Clean	`O=C1NC(=O)/C(=C\c2cccc(O)c2)N1`
ZINC1875304352	0.667	297.4 Da LogP 1.49 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1N[C@H](Cc2c[nH]c3ccccc23)C(=O)N[C@H]1CC1CC1`
ZINC2069462964	0.667	297.4 Da LogP 1.49 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1N[C@@H](CC2CC2)C(=O)N[C@H]1Cc1c[nH]c2ccccc12`
ZINC208759478	0.667	319.4 Da LogP 2.07 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1N[C@H](Cc2c[nH]c3ccccc23)C(=O)N[C@H]1c1cccc…`
ZINC208759513	0.667	319.4 Da LogP 2.07 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1N[C@@H](c2ccccc2)C(=O)N[C@H]1Cc1c[nH]c2cccc…`
ZINC2819805	0.667	218.2 Da LogP 0.21 TPSA 75.3	✓ Ro5	✓ Clean	`O=C1NC(=O)C(Cc2ccccc2)C(=O)N1`
ZINC39365597	0.667	319.4 Da LogP 2.07 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1N[C@H](c2ccccc2)C(=O)N[C@H]1Cc1c[nH]c2ccccc…`
ZINC670451826	0.667	283.3 Da LogP 1.10 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1N[C@H](Cc2c[nH]c3ccccc23)C(=O)N[C@H]1C1CC1`
ZINC72182	0.667	206.2 Da LogP 1.01 TPSA 58.2	✓ Ro5	✓ Clean	`O=C1NC(=O)/C(=C\c2cccc(F)c2)N1`
ZINC828321135	0.667	283.3 Da LogP 1.10 TPSA 74.0	✓ Ro5	✓ Clean	`O=C1N[C@@H](C2CC2)C(=O)N[C@H]1Cc1c[nH]c2ccccc12`

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.