Protein profile

PA2739

phenylalanine--tRNA ligase subunit beta

Genome: NC_002516.2

Gene: PA2739 pheT Structure source: Experimental + AlphaFold UniProt Q9I0A4

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Amino acids 792

Annotations 8

Features 54

PDB binders 4

Druggability 0.767

Overview

Basic information about this protein and its source genome.

Accession: PA2739
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA2739 pheT
Status: annotated
Amino acids: 792
Structure source: Experimental + AlphaFold

6.1.1.20

GO:0009328 An enzyme complex that catalyzes the ligation of phenylalanine to tRNA(Phe), forming L-phenylalanyl-tRNA(Phe). GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0000287 Binding to a magnesium (Mg) ion. GO:0004826 Catalysis of the reaction: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe). GO:0000049 Binding to a transfer RNA. GO:0006432 The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. The phenylalanyl-tRNA synthetase is a class-II synthetase. However, unlike other class II enzymes, The activated amino acid is transferred to the 2'-OH group of a phenylalanine-accepting tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 23.59
Human E-value: 1.27e-18
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 0.767

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

6.1.1.20

Gene Ontology (GO)

GO:0009328 An enzyme complex that catalyzes the ligation of phenylalanine to tRNA(Phe), forming L-phenylalanyl-tRNA(Phe).
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0000287 Binding to a magnesium (Mg) ion.
GO:0004826 Catalysis of the reaction: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe).
GO:0000049 Binding to a transfer RNA.
GO:0006432 The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. The phenylalanyl-tRNA synthetase is a class-II synthetase. However, unlike other class II enzymes, The activated amino acid is transferred to the 2'-OH group of a phenylalanine-accepting tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
GO:0003723 Binding to an RNA molecule or a portion thereof.

Sequence Features

Domain/signature hits from InterPro and related databases.

54 records

Show feature table

Start	End	DB	Term	Name
405	471	Pfam	PF03484	tRNA synthetase B5 domain
405	471	InterPro	IPR005147	tRNA synthetase, B5-domain
45	144	Pfam	PF01588	Putative tRNA binding domain
45	144	InterPro	IPR002547	tRNA-binding domain
698	791	Pfam	PF03147	Ferredoxin-fold anticodon binding domain
698	791	InterPro	IPR005121	Ferrodoxin-fold anticodon-binding domain
699	792	FunFam	G3DSA:3.30.70.380:FF:000001	Phenylalanine--tRNA ligase beta subunit
506	683	CDD	cd00769	PheRS_beta_core
506	683	InterPro	IPR041616	Phenylalanyl tRNA synthetase beta chain, core domain
39	147	ProSiteProfiles	PS50886	tRNA-binding domain profile.
39	147	InterPro	IPR002547	tRNA-binding domain
401	475	FunFam	G3DSA:3.30.56.10:FF:000002	Phenylalanine--tRNA ligase beta subunit
692	791	SUPERFAMILY	SSF54991	Anticodon-binding domain of PheRS
692	791	InterPro	IPR036690	Ferrodoxin-fold anticodon-binding domain superfamily
2	683	PANTHER	PTHR10947	PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN AND LEUCINE-RICH REPEAT-CONTAINING PROTEIN 47
2	683	InterPro	IPR045060	Phenylalanine-tRNA ligase, class IIc, beta subunit
195	394	SUPERFAMILY	SSF56037	PheT/TilS domain
400	476	ProSiteProfiles	PS51483	B5 domain profile.
400	476	InterPro	IPR005147	tRNA synthetase, B5-domain
6	181	Gene3D	G3DSA:3.30.56.10	-
1	791	NCBIfam	TIGR00472	phenylalanine--tRNA ligase subunit beta
1	791	InterPro	IPR004532	Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type
487	689	FunFam	G3DSA:3.30.930.10:FF:000022	Phenylalanine--tRNA ligase beta subunit
1	785	Hamap	MF_00283	Phenylalanine--tRNA ligase beta subunit [pheT].
1	785	InterPro	IPR004532	Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type
467	683	SUPERFAMILY	SSF55681	Class II aaRS and biotin synthetases
467	683	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
196	394	Gene3D	G3DSA:3.50.40.10	-
196	394	InterPro	IPR020825	Phenylalanyl-tRNA synthetase-like, B3/B4
400	475	Gene3D	G3DSA:3.30.56.10	-
698	791	ProSiteProfiles	PS51447	Ferredoxin-fold anticodon binding (FDX-ACB) domain profile.
39	190	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
39	190	InterPro	IPR012340	Nucleic acid-binding, OB-fold
485	690	Gene3D	G3DSA:3.30.930.10	Bira Bifunctional Protein; Domain 2
485	690	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
474	681	Pfam	PF17759	Phenylalanyl tRNA synthetase beta chain CLM domain
474	681	InterPro	IPR041616	Phenylalanyl tRNA synthetase beta chain, core domain
403	475	SUPERFAMILY	SSF46955	Putative DNA-binding domain
403	475	InterPro	IPR009061	Putative DNA-binding domain superfamily
699	792	Gene3D	G3DSA:3.30.70.380	-
699	792	InterPro	IPR036690	Ferrodoxin-fold anticodon-binding domain superfamily
39	153	FunFam	G3DSA:2.40.50.140:FF:000045	Phenylalanine--tRNA ligase beta subunit
45	146	CDD	cd02796	tRNA_bind_bactPheRS
45	146	InterPro	IPR033714	Phenylalanly tRNA synthetase, tRNA-binding-domain
211	384	SMART	SM00873	B3_4_2
211	384	InterPro	IPR005146	B3/B4 tRNA-binding domain
39	153	Gene3D	G3DSA:2.40.50.140	-
39	153	InterPro	IPR012340	Nucleic acid-binding, OB-fold
402	471	SMART	SM00874	B5_2
402	471	InterPro	IPR005147	tRNA synthetase, B5-domain
211	383	Pfam	PF03483	B3/4 domain
211	383	InterPro	IPR005146	B3/B4 tRNA-binding domain
698	791	SMART	SM00896	FDX_ACB_2
195	396	FunFam	G3DSA:3.50.40.10:FF:000001	Phenylalanine--tRNA ligase beta subunit

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

5 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
PDB 4P72	X-ray	2.62 Å	A,B	100.0% 1-792	PDBe RCSB PDBj File	Viewing
PDB 4P74	X-ray	2.70 Å	A,B	100.0% 1-792	PDBe RCSB PDBj File	Loaded
PDB 4P71	X-ray	2.79 Å	A,B	100.0% 1-792	PDBe RCSB PDBj File	Loaded
PDB 4P75	X-ray	2.96 Å	A,B	100.0% 1-792	PDBe RCSB PDBj File	Loaded
PDB 4P73	X-ray	3.03 Å	A,B	100.0% 1-792	PDBe RCSB PDBj File	Loaded
AlphaFold PA2739	AlphaFold	—	—	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
1				0.767

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				22.46	0.881
2				2.33	0.06

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				0.621
4				0.387

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.

54 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
DAH	3TEH	P27002	197.2 Da LogP 0.05 TPSA 103.8	✓ Ro5	Alert	`c1cc(c(cc1C[C@@H](C(=O)O)N)O)O`
MTY	3HFZ	Q5SGX1	181.2 Da LogP 0.35 TPSA 83.5	✓ Ro5	✓ Clean	`c1cc(cc(c1)O)C[C@@H](C(=O)O)N`
PUY	4TVA	Q5SGX1	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`CN(C)c1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H]…`
TAM	3ICA	Q7MXR4	163.2 Da LogP -1.17 TPSA 86.7	✓ Ro5	✓ Clean	`C(CO)C(CCO)(CCO)N`

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
ZINC53147178	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@@H…`
ZINC53147179	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@@H]…`
ZINC58994963	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@@H]…`
ZINC59065899	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](O)[C@@H](n…`
ZINC59817042	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@H](…`
ZINC59817043	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@H]2[C@H](O)[C@@H](n3…`
ZINC59817045	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@H]2[C@H](O)[C@H](n3c…`
ZINC61389312	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@H](…`
ZINC71789712	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@H]…`
ZINC73333306	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@H](n…`
ZINC73333309	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@@H](…`
ZINC73333313	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@H]2[C@H](O)[C@@H](n3c…`
ZINC73333316	1.000	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@H]2[C@H](O)[C@H](n3cn…`
ZINC4830897	0.829	443.5 Da LogP -1.28 TPSA 183.7	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@H](n…`
ZINC4830899	0.829	443.5 Da LogP -1.28 TPSA 183.7	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@H](…`
ZINC4830900	0.829	443.5 Da LogP -1.28 TPSA 183.7	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@H]2[C@H](CO)O[C@H](n3…`
ZINC4830901	0.829	443.5 Da LogP -1.28 TPSA 183.7	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@H]2[C@H](CO)O[C@H](n…`
ZINC1775953634	0.824	495.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`C#CCOc1ccc(C[C@H](N)C(=O)N[C@H]2[C@@H](CO)O[C@@…`
ZINC205891530	0.824	495.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`C#CCOc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@…`
ZINC221530727	0.824	495.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`C#CCOc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@…`
ZINC221530830	0.824	495.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`C#CCOc1ccc(C[C@@H](N)C(=O)N[C@H]2[C@H](O)[C@@H]…`
ZINC222589180	0.824	495.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`C#CCOc1ccc(C[C@H](N)C(=O)N[C@H]2[C@@H](CO)O[C@@…`
ZINC669678878	0.824	495.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`C#CCOc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](O)[C@@H…`
ZINC403598	0.800	273.3 Da LogP 2.14 TPSA 92.8	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(Oc2ccc(O)cc2)cc1)C(=O)O`
ZINC403599	0.800	273.3 Da LogP 2.14 TPSA 92.8	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(Oc2ccc(O)cc2)cc1)C(=O)O`
ZINC1834294	0.793	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(C[C@H](N)C(=O)O)c1)C(=O)O`
ZINC1834295	0.793	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(C[C@@H](N)C(=O)O)c1)C(=O)O`
ZINC1834297	0.793	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](Cc1cccc(C[C@@H](N)C(=O)O)c1)C(=O)O`
ZINC113264413	0.778	317.4 Da LogP 3.98 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccc(-c3ccccc3)cc2)cc1)C(=O)O`
ZINC113264415	0.778	317.4 Da LogP 3.98 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(-c2ccc(-c3ccccc3)cc2)cc1)C(=O)O`
ZINC2244337	0.778	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccccc2)cc1)C(=O)O`
ZINC2244338	0.778	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(-c2ccccc2)cc1)C(=O)O`
ZINC2512061	0.774	360.4 Da LogP 0.67 TPSA 167.1	1 viol.	✓ Clean	`N[C@@H](Cc1ccc(O)c(-c2cc(C[C@H](N)C(=O)O)ccc2O)…`
ZINC53188912	0.753	485.5 Da LogP -0.45 TPSA 152.1	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N(C)[C@@H]2[C@H](CO)O[C@…`
ZINC53188914	0.753	485.5 Da LogP -0.45 TPSA 152.1	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N(C)[C@@H]2[C@H](CO)O[C@…`
ZINC53188917	0.753	485.5 Da LogP -0.45 TPSA 152.1	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N(C)[C@H]2[C@H](O)[C@@H]…`
ZINC53188920	0.753	485.5 Da LogP -0.45 TPSA 152.1	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N(C)[C@H]2[C@H](O)[C@H](…`
ZINC39351856	0.741	328.4 Da LogP 1.26 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccc(C[C@H](N)C(=O)O)cc2)cc1)C…`
ZINC2561081	0.724	269.3 Da LogP 1.87 TPSA 80.4	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(C(=O)c2ccccc2)cc1)C(=O)O`
ZINC2561082	0.724	269.3 Da LogP 1.87 TPSA 80.4	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(C(=O)c2ccccc2)cc1)C(=O)O`
ZINC113539705	0.700	265.3 Da LogP 2.04 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(C#Cc2ccccc2)cc1)C(=O)O`
ZINC113539708	0.700	265.3 Da LogP 2.04 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(C#Cc2ccccc2)cc1)C(=O)O`
ZINC116910786	0.700	269.3 Da LogP 3.06 TPSA 88.0	✓ Ro5	Alert	`N[C@@H](Cc1ccc(/N=N/c2ccccc2)cc1)C(=O)O`
ZINC29566843	0.700	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1cccc(-c2ccccc2)c1)C(=O)O`
ZINC29570997	0.700	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1cccc(-c2ccccc2)c1)C(=O)O`
ZINC44283581	0.700	257.3 Da LogP 2.43 TPSA 72.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(Oc2ccccc2)cc1)C(=O)O`
ZINC44283583	0.700	257.3 Da LogP 2.43 TPSA 72.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(Oc2ccccc2)cc1)C(=O)O`
ZINC2111574	0.692	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1C[C@H](N)C(=O)O)C(=O)O`
ZINC2111575	0.692	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1C[C@@H](N)C(=O)O)C(=O)O`
ZINC2111578	0.692	252.3 Da LogP -0.40 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1C[C@@H](N)C(=O)O)C(=O)O`

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.