Protein profile

PA3556

4-amino-4-deoxy-L-arabinose lipid A transferase

Genome: NC_002516.2

Gene: PA3556 arnT Structure source: AlphaFold UniProt Q9HY61

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Amino acids 549

Annotations 10

Features 46

PDB binders 4

Druggability 0.883

Overview

Basic information about this protein and its source genome.

Accession: PA3556
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA3556 arnT
Status: annotated
Amino acids: 549
Structure source: AlphaFold

2.4.2.43

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:0103015 Catalysis of the reaction: (Kdo)2-lipid A + 2 4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,poly-cis-undecaprenyl phosphate = (beta-L-Ara4N)2-(KDO)2-lipid A + 2 ditrans,polycis-undecaprenyl phosphate. GO:0000030 Catalysis of the transfer of a mannosyl group to an acceptor molecule, typically another carbohydrate or a lipid. GO:0016763 Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor). GO:0009245 The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common. GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.

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 0.883

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

2.4.2.43

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:0103015 Catalysis of the reaction: (Kdo)2-lipid A + 2 4-amino-4-deoxy-alpha-L-arabinopyranosyl di-trans,poly-cis-undecaprenyl phosphate = (beta-L-Ara4N)2-(KDO)2-lipid A + 2 ditrans,polycis-undecaprenyl phosphate.
GO:0000030 Catalysis of the transfer of a mannosyl group to an acceptor molecule, typically another carbohydrate or a lipid.
GO:0016763 Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
GO:0009245 The chemical reactions and pathways resulting in the formation of lipid A, the glycolipid group of bacterial lipopolysaccharides, consisting of four to six fatty acyl chains linked to two glucosamine residues. Further modifications of the backbone are common.
GO:0009103 The chemical reactions and pathways resulting in the formation of lipopolysaccharides, any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria.
GO:0006493 A glycoprotein biosynthetic process starting with the covalent linkage of carbohydrate or carbohydrate derivative unit via a glycosidic bond to the oxygen atom of a serine, threonine, hydroxylysine, hydroxyproline or tyrosine side chain in a protein, which can be further elongated with the sequential addition of sugar units resulting in the formation of a protein O-linked glycan.
GO:0010041 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an iron(III) ion stimulus.
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.

46 records

Show feature table

Start	End	DB	Term	Name
257	279	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
225	256	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	25	SignalP_EUK	SignalP-noTM	SignalP-noTM
81	101	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
315	335	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
7	29	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
204	226	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
182	197	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
133	137	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
113	132	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
160	176	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
204	224	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
397	402	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
378	396	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
336	346	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
280	290	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
6	530	PANTHER	PTHR33908	MANNOSYLTRANSFERASE YKCB-RELATED
10	236	Pfam	PF02366	Dolichyl-phosphate-mannose-protein mannosyltransferase
10	236	InterPro	IPR003342	Glycosyl transferase family 39/83
313	332	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
378	400	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
367	377	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
154	159	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
175	197	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	22	Phobius	SIGNAL_PEPTIDE	Signal peptide region
80	102	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
422	549	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
341	363	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
198	203	Phobius	CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
177	181	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
257	279	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
138	153	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	5	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
403	421	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
407	426	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
1	547	Hamap	MF_01165	Undecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferase [arnT].
1	547	InterPro	IPR022839	Undecaprenyl phosphate-alpha-4-amino-4-deoxy-L-arabinose arabinosyl transferase
291	309	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
6	17	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
23	80	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
347	366	Phobius	TRANSMEMBRANE	Region of a membrane-bound protein predicted to be embedded in the membrane.
291	308	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
18	22	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
310	314	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
115	132	TMHMM	TMhelix	Region of a membrane-bound protein predicted to be embedded in the membrane.
102	112	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

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA3556	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
3				0.883
2				0.782
6				0.678
7				0.434

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
5TR	5F15	Q1LDT6	847.3 Da LogP 18.33 TPSA 66.8	2 viol.	✓ Clean	`CC(=CCC/C(=C/CC/C(=C/CC/C(=C/CC/C(=C\CC/C(=C/CC…`
DSL	5EZM	Q1LDT6	779.2 Da LogP 16.60 TPSA 66.8	2 viol.	✓ Clean	`CC(=CCC/C(=C/CC/C(=C\CC/C(=C\CC/C(=C\CC/C(=C\CC…`
MPG	5EZM	Q1LDT6	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCCCCOC(=O)[C@@H](CO)O`
PC	5EZM	Q1LDT6	184.2 Da LogP -0.20 TPSA 66.8	✓ Ro5	✓ Clean	`C[N+](C)(C)CCOP(=O)(O)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
CHEMBL255766	O52327	—	301.3 Da LogP 0.45 TPSA 136.9	✓ Ro5	Alert	`CC(=O)OC1OC[C@H](N=[N+]=[N-])[C@H](OC(C)=O)[C@H…`

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
ZINC2556391	1.000	302.4 Da LogP 4.51 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/COP(=O)(O)O`
ZINC1532829	0.964	234.2 Da LogP 2.79 TPSA 66.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/COP(=O)(O)O`
ZINC12494625	0.765	382.3 Da LogP 4.63 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/CO[P@@](=O)(O)OP(=O)…`
ZINC2356589248	0.765	382.3 Da LogP 4.63 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCCC(C)=CCCC(C)=CCO[P@](=O)(O)OP(=O)(O)O`
ZINC8215849	0.735	314.2 Da LogP 2.91 TPSA 113.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CO[P@@](=O)(O)OP(=O)(O)O`
ZINC8218174	0.722	462.3 Da LogP 4.75 TPSA 159.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/CO[P@@](=O)(O)O[P@@]…`
ZINC71404870	0.719	230.3 Da LogP 4.23 TPSA 26.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/COP(C)(C)=O`
ZINC34661063	0.694	394.2 Da LogP 3.02 TPSA 159.8	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CO[P@@](=O)(O)O[P@@](=O)(O)OP(…`
ZINC59725075	0.629	226.4 Da LogP 4.25 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCC/C=C/CCCCOC(C)=O`
ZINC59725096	0.629	226.4 Da LogP 4.25 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCC/C=C\CCCCOC(C)=O`
ZINC103619636	0.611	340.3 Da LogP 1.54 TPSA 176.4	✓ Ro5	Alert	`CC(=O)O[C@H]1[C@H](N=[N+]=[N-])C[C@H](N=[N+]=[N…`
ZINC102279436	0.600	358.5 Da LogP 4.54 TPSA 72.8	✓ Ro5	✓ Clean	`CCCCCCCCOC(=O)C[C@H](O)C(=O)OCCCCCCCC`
ZINC102279441	0.600	358.5 Da LogP 4.54 TPSA 72.8	✓ Ro5	✓ Clean	`CCCCCCCCOC(=O)C[C@@H](O)C(=O)OCCCCCCCC`
ZINC1719908	0.588	264.4 Da LogP 4.97 TPSA 26.3	✓ Ro5	✓ Clean	`CC(=O)OC/C=C(\C)CC/C=C(\C)CCC=C(C)C`
ZINC1857777740	0.588	264.4 Da LogP 4.97 TPSA 26.3	✓ Ro5	✓ Clean	`CC(=O)OCC=C(C)CCC=C(C)CCC=C(C)C`
ZINC4480023	0.588	264.4 Da LogP 4.97 TPSA 26.3	✓ Ro5	✓ Clean	`CC(=O)OC/C=C(/C)CC/C=C(/C)CCC=C(C)C`
ZINC5829138	0.588	264.4 Da LogP 4.97 TPSA 26.3	✓ Ro5	✓ Clean	`CC(=O)OC/C=C(/C)CC/C=C(\C)CCC=C(C)C`
ZINC5829142	0.588	264.4 Da LogP 4.97 TPSA 26.3	✓ Ro5	✓ Clean	`CC(=O)OC/C=C(\C)CC/C=C(/C)CCC=C(C)C`
ZINC1850172	0.583	240.4 Da LogP 4.64 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCC/C=C/CCCOC(C)=O`
ZINC2018958	0.583	226.4 Da LogP 4.25 TPSA 26.3	✓ Ro5	✓ Clean	`CCCC/C=C/CCCCCCOC(C)=O`
ZINC43068418	0.583	240.4 Da LogP 4.64 TPSA 26.3	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCOC(C)=O`
ZINC4543853	0.583	226.4 Da LogP 4.25 TPSA 26.3	✓ Ro5	✓ Clean	`CCCC/C=C\CCCCCCOC(C)=O`
ZINC100503505	0.581	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCC(=O)OCCC[C@H](O)CO`
ZINC100503506	0.581	356.5 Da LogP 4.92 TPSA 66.8	✓ Ro5	✓ Clean	`CCCCCCCC/C=C\CCCCCC(=O)OCCC[C@@H](O)CO`
ZINC17000749	0.571	265.4 Da LogP 4.50 TPSA 52.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C\CC/C(C)=C\COC(N)=O`
ZINC17000752	0.571	265.4 Da LogP 4.50 TPSA 52.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C\COC(N)=O`
ZINC17000755	0.571	265.4 Da LogP 4.50 TPSA 52.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C\CC/C(C)=C/COC(N)=O`
ZINC17000758	0.571	265.4 Da LogP 4.50 TPSA 52.3	✓ Ro5	✓ Clean	`CC(C)=CCC/C(C)=C/CC/C(C)=C/COC(N)=O`
ZINC5291871	0.561	301.3 Da LogP 0.45 TPSA 136.9	✓ Ro5	Alert	`CC(=O)O[C@H]1[C@H](OC(C)=O)CO[C@@H](N=[N+]=[N-]…`
ZINC101342141	0.559	374.5 Da LogP 3.52 TPSA 93.1	✓ Ro5	✓ Clean	`CCCCCCCCOC(=O)[C@@H](O)[C@@H](O)C(=O)OCCCCCCCC`
ZINC101342142	0.559	374.5 Da LogP 3.52 TPSA 93.1	✓ Ro5	✓ Clean	`CCCCCCCCOC(=O)[C@@H](O)[C@H](O)C(=O)OCCCCCCCC`
ZINC101342143	0.559	374.5 Da LogP 3.52 TPSA 93.1	✓ Ro5	✓ Clean	`CCCCCCCCOC(=O)[C@H](O)[C@@H](O)C(=O)OCCCCCCCC`
ZINC1319000	0.556	318.3 Da LogP -0.30 TPSA 114.4	✓ Ro5	✓ Clean	`CC(=O)O[C@@H]1OC[C@@H](OC(C)=O)[C@H](OC(C)=O)[C…`
ZINC14584247	0.556	318.3 Da LogP -0.30 TPSA 114.4	✓ Ro5	✓ Clean	`CC(=O)O[C@H]1CO[C@H](OC(C)=O)[C@@H](OC(C)=O)[C@…`
ZINC2003180	0.556	318.3 Da LogP -0.30 TPSA 114.4	✓ Ro5	✓ Clean	`CC(=O)O[C@H]1CO[C@H](OC(C)=O)[C@H](OC(C)=O)[C@H…`
ZINC212206827	0.556	273.4 Da LogP 2.77 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCOC(=O)[C@@H](N)CO`
ZINC25628116	0.556	318.3 Da LogP -0.30 TPSA 114.4	✓ Ro5	✓ Clean	`CC(=O)O[C@H]1[C@H](OC(C)=O)CO[C@H](OC(C)=O)[C@@…`
ZINC39336225	0.556	318.3 Da LogP -0.30 TPSA 114.4	✓ Ro5	✓ Clean	`CC(=O)O[C@@H]1[C@H](OC(C)=O)[C@@H](OC(C)=O)OC[C…`
ZINC4557393	0.556	318.3 Da LogP -0.30 TPSA 114.4	✓ Ro5	✓ Clean	`CC(=O)O[C@@H]1CO[C@H](OC(C)=O)[C@H](OC(C)=O)[C@…`
ZINC4557394	0.556	318.3 Da LogP -0.30 TPSA 114.4	✓ Ro5	✓ Clean	`CC(=O)O[C@H]1CO[C@H](OC(C)=O)[C@H](OC(C)=O)[C@@…`
ZINC4557395	0.556	318.3 Da LogP -0.30 TPSA 114.4	✓ Ro5	✓ Clean	`CC(=O)O[C@@H]1OC[C@@H](OC(C)=O)[C@@H](OC(C)=O)[…`
ZINC4557396	0.556	318.3 Da LogP -0.30 TPSA 114.4	✓ Ro5	✓ Clean	`CC(=O)O[C@H]1CO[C@@H](OC(C)=O)[C@H](OC(C)=O)[C@…`
ZINC5438146	0.556	318.3 Da LogP -0.30 TPSA 114.4	✓ Ro5	✓ Clean	`CC(=O)O[C@@H]1OC[C@@H](OC(C)=O)[C@@H](OC(C)=O)[…`
ZINC5495606	0.556	318.3 Da LogP -0.30 TPSA 114.4	✓ Ro5	✓ Clean	`CC(=O)O[C@@H]1[C@@H](OC(C)=O)OC[C@@H](OC(C)=O)[…`
ZINC77300481	0.553	260.3 Da LogP 2.12 TPSA 83.8	✓ Ro5	✓ Clean	`CCCCCCCCOC(=O)[C@H](O)CCC(=O)O`
ZINC77300485	0.553	260.3 Da LogP 2.12 TPSA 83.8	✓ Ro5	✓ Clean	`CCCCCCCCOC(=O)[C@@H](O)CCC(=O)O`
ZINC113027531	0.548	310.4 Da LogP 3.58 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCCCCCO[P@](=O)(O)OCC[N+](C)(C)C`
ZINC1560408744	0.548	257.2 Da LogP -0.28 TPSA 96.2	✓ Ro5	✓ Clean	`C[N+](C)(C)CCO[P@](=O)(O)OC[C](O)CO`
ZINC217410460	0.548	338.4 Da LogP 4.36 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCO[P@@](=O)(O)OCC[N+](C)(C)C`
ZINC43562168	0.548	352.5 Da LogP 4.75 TPSA 55.8	✓ Ro5	✓ Clean	`CCCCCCCCCCCCO[P@@](=O)(O)OCC[N+](C)(C)C`

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.