Protein profile

PA4119

aminoglycoside 3-N-acetyltransferase

Genome: NC_002516.2

Gene: aph PA4119 Structure source: AlphaFold UniProt Q9HWR2

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Amino acids 268

Annotations 6

Features 11

PDB binders 13

Druggability 0.584

Overview

Basic information about this protein and its source genome.

Accession: PA4119
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: aph PA4119
Status: annotated
Amino acids: 268
Structure source: AlphaFold

2.7.1.95

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0008910 Catalysis of the reaction: ATP + kanamycin = ADP + 2 H+ + kanamycin 3'-phosphate. GO:0046872 Binding to a metal ion. GO:0046677 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 antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms. GO:0016773 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).

Target profile

Computed evidence for target prioritization.

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

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 0.584

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

2.7.1.95

Gene Ontology (GO)

GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0008910 Catalysis of the reaction: ATP + kanamycin = ADP + 2 H+ + kanamycin 3'-phosphate.
GO:0046872 Binding to a metal ion.
GO:0046677 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 antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
GO:0016773 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records

Show feature table

Start	End	DB	Term	Name
14	267	SUPERFAMILY	SSF56112	Protein kinase-like (PK-like)
14	267	InterPro	IPR011009	Protein kinase-like domain superfamily
30	258	Pfam	PF01636	Phosphotransferase enzyme family
30	258	InterPro	IPR002575	Aminoglycoside phosphotransferase
3	268	PIRSF	PIRSF000706	Kanamycin_kin
3	268	InterPro	IPR024165	Aminoglycoside 3-phosphotransferase
4	96	Gene3D	G3DSA:3.30.200.20	Phosphorylase Kinase; domain 1
48	245	PANTHER	PTHR21310	AMINOGLYCOSIDE PHOSPHOTRANSFERASE-RELATED-RELATED
23	268	CDD	cd05150	APH
23	268	InterPro	IPR024165	Aminoglycoside 3-phosphotransferase
99	268	Gene3D	G3DSA:3.90.1200.10	-

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 + 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 PA4119	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				0.584

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.

63 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
51G	5IQC	P0A0C1	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`C[C@H]([C@@H]1CC[C@H]([C@H](O1)O[C@@H]2[C@H](C[…`
84D	6CAV	P0A0C1	451.5 Da LogP -5.27 TPSA 247.9	2 viol.	✓ Clean	`C1C[C@H]([C@H](O[C@@H]1CN)O[C@@H]2[C@H](C[C@H](…`
84G	6CGG	P0A0C1	552.6 Da LogP -6.40 TPSA 297.3	3 viol.	✓ Clean	`C1C[C@H]([C@H](O[C@@H]1CN)O[C@@H]2[C@H](C[C@H](…`
AKN	6CGD	P0A0C1	585.6 Da LogP -8.42 TPSA 331.9	3 viol.	✓ Clean	`C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1NC(=O)[C@H](…`
ANP	1J7U	P0A3Y5	506.2 Da LogP -2.06 TPSA 281.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
B31	3TM0	P0A3Y5	555.6 Da LogP -7.79 TPSA 311.7	3 viol.	✓ Clean	`C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1NC(=O)[C@H](…`
CKI	3Q2J	P0A3Y5	285.8 Da LogP 1.13 TPSA 85.1	✓ Ro5	✓ Clean	`c1cc(c2ccncc2c1S(=O)(=O)NCCN)Cl`
GCP	5BYL	P0A0C1	521.2 Da LogP -2.22 TPSA 289.9	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…`
GNP	5IQI	P0A0C1	522.2 Da LogP -2.76 TPSA 301.9	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…`
KAN	1ND4	P00552	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…`
LIV	6CEY	P0A0C1	761.8 Da LogP -10.01 TPSA 406.2	3 viol.	✓ Clean	`C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…`
NMY	5IQE	P0A0C1	614.7 Da LogP -8.90 TPSA 353.1	3 viol.	✓ Clean	`C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…`
RIO	5IQD	P0A0C1	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…`

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
ZINC100505442	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H](C)[C@H]1CC[C@@H](N)[C@@H](O[C@H]2[C@@H]…`
ZINC100505444	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H](C)[C@H]1CC[C@@H](N)[C@@H](O[C@@H]2[C@@H…`
ZINC100505446	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H](C)[C@H]1CC[C@@H](N)[C@@H](O[C@H]2[C@@H]…`
ZINC15449121	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H](C)[C@@H]1CC[C@@H](N)[C@@H](O[C@@H]2[C@@…`
ZINC17654095	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@…`
ZINC1857793042	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC2382315406	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@@H](C)[C@@H]1CC[C@H](N)[C@H](O[C@H]2[C@@H]…`
ZINC239203289	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC239203290	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC239203291	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC239203292	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC242437511	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H](C)[C@@H]1CC[C@H](N)[C@H](O[C@@H]2[C@H](…`
ZINC242437512	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H](C)[C@@H]1CC[C@H](N)[C@H](O[C@H]2[C@H](O…`
ZINC242437513	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H](C)[C@@H]1CC[C@H](N)[C@H](O[C@@H]2[C@H](…`
ZINC242437514	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H](C)[C@@H]1CC[C@H](N)[C@H](O[C@H]2[C@H](O…`
ZINC242649355	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649358	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649360	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649362	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC245224172	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224173	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224174	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224175	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC38139393	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H](C)[C@@H]1CC[C@@H](N)[C@@H](O[C@H]2[C@@H…`
ZINC43470138	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H…`
ZINC6415144	1.000	285.8 Da LogP 1.13 TPSA 85.1	✓ Ro5	✓ Clean	`NCCNS(=O)(=O)c1ccc(Cl)c2ccncc12`
ZINC8101114	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@@H](C)[C@@H]1CC[C@H](N)[C@H](O[C@@H]2[C@H]…`
ZINC8101115	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC8101116	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@@H](C)[C@H]1CC[C@H](N)[C@H](O[C@@H]2[C@H](…`
ZINC8101117	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC8101132	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@H]3O…`
ZINC8101133	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@H]3O…`
ZINC8101134	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@H](O[C@H]3O[…`
ZINC8101135	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@H](O[C@H]3O[…`
ZINC8143541	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H](C)[C@@H]1CC[C@@H](N)[C@@H](O[C@@H]2[C@@…`
ZINC8214392	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@@H](C)[C@@H]1CC[C@@H](N)[C@@H](O[C@@H]2[C@…`
ZINC8214590	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC8214768	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H](C)[C@@H]1CC[C@@H](N)[C@@H](O[C@H]2[C@@H…`
ZINC8217403	1.000	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC85548539	1.000	477.6 Da LogP -3.33 TPSA 199.7	2 viol.	✓ Clean	`CN[C@H](C)[C@H]1CC[C@@H](N)[C@@H](O[C@@H]2[C@@H…`
ZINC100052153	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC100223147	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@@H](O[C@@H]3O[C@H](…`
ZINC242575106	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@@H]3O[C@H](CO…`
ZINC242575107	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@@H]3O[C@H](CO…`
ZINC242575108	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@@H]3O[C@H](CO…`
ZINC242575109	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@@H]3O[C@H](CO…`
ZINC43664300	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@H]3O[C@@H](CO…`
ZINC43664303	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@H]3O[C@@H](CO…`
ZINC53255716	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC56874669	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`

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.