Protein profile

PA0668

tyrosine--tRNA ligase

Genome: NC_002516.2

Gene: tyrZ Structure source: ColabFold

Export view

Amino acids 399

Annotations 7

Features 30

PDB binders 7

Druggability 0.367

Overview

Basic information about this protein and its source genome.

Accession: PA0668
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: tyrZ
Status: annotated
Amino acids: 399
Structure source: ColabFold

GO:0006437 The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-tRNA synthetase. The tyrosyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tyrosine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification. GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0004831 Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H+. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 30.833
Human E-value: 2.55e-22
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 0.367

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0006437 The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-tRNA synthetase. The tyrosyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tyrosine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0004831 Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H+.
GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
GO:0006418 The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, to be used in ribosome-mediated polypeptide synthesis.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records

Show feature table

Start	End	DB	Term	Name
42	52	ProSitePatterns	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.
42	52	InterPro	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site
11	392	PANTHER	PTHR11766	TYROSYL-TRNA SYNTHETASE
11	392	InterPro	IPR024088	Tyrosine-tRNA ligase, bacterial-type
323	387	Gene3D	G3DSA:3.10.290.10	-
323	387	InterPro	IPR036986	RNA-binding S4 domain superfamily
336	396	ProSiteProfiles	PS50889	S4 RNA-binding domain profile.
2	218	FunFam	G3DSA:3.40.50.620:FF:000061	Tyrosine--tRNA ligase
178	200	PRINTS	PR01040	Tyrosyl-tRNA synthetase signature
178	200	InterPro	IPR002307	Tyrosine-tRNA ligase
211	223	PRINTS	PR01040	Tyrosyl-tRNA synthetase signature
211	223	InterPro	IPR002307	Tyrosine-tRNA ligase
46	68	PRINTS	PR01040	Tyrosyl-tRNA synthetase signature
46	68	InterPro	IPR002307	Tyrosine-tRNA ligase
161	176	PRINTS	PR01040	Tyrosyl-tRNA synthetase signature
161	176	InterPro	IPR002307	Tyrosine-tRNA ligase
219	322	Gene3D	G3DSA:1.10.240.10	-
34	298	CDD	cd00805	TyrRS_core
34	298	InterPro	IPR002307	Tyrosine-tRNA ligase
4	310	SUPERFAMILY	SSF52374	Nucleotidylyl transferase
31	315	Pfam	PF00579	tRNA synthetases class I (W and Y)
31	315	InterPro	IPR002305	Aminoacyl-tRNA synthetase, class Ic
2	396	Hamap	MF_02007	Tyrosine--tRNA ligase [tyrS].
2	396	InterPro	IPR024108	Tyrosine-tRNA ligase, bacterial-type, type 2
219	325	FunFam	G3DSA:1.10.240.10:FF:000006	Tyrosine--tRNA ligase
320	396	SUPERFAMILY	SSF55174	Alpha-L RNA-binding motif
2	396	NCBIfam	TIGR00234	tyrosine--tRNA ligase
2	396	InterPro	IPR002307	Tyrosine-tRNA ligase
2	218	Gene3D	G3DSA:3.40.50.620	HUPs
2	218	InterPro	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold

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...

Legend High Medium Low

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
ColabFold PA0668	ColabFold	—	—	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				0.367
1				0.221

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.

65 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
AZY	2YXN	P0AGJ9	222.2 Da LogP 1.29 TPSA 132.3	✓ Ro5	Alert	`c1cc(c(cc1C[C@@H](C(=O)O)N)N=[N+]=[N-])O`
IYR	1WQ3	P0AGJ9	307.1 Da LogP 0.95 TPSA 83.5	✓ Ro5	✓ Clean	`c1cc(c(cc1C[C@@H](C(=O)O)N)I)O`
TYE	1H3E	P83453	167.2 Da LogP 0.25 TPSA 66.5	✓ Ro5	✓ Clean	`c1cc(ccc1C[C@@H](CO)N)O`
TYS	6WN2	P0AGJ9	261.3 Da LogP -0.18 TPSA 126.9	✓ Ro5	✓ Clean	`c1cc(ccc1C[C@@H](C(=O)O)N)OS(=O)(=O)O`
Y3U	6HB7	P0AGJ9	500.5 Da LogP -3.18 TPSA 212.4	2 viol.	✓ Clean	`CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…`
YSA	1VBM	P0AGJ9	509.5 Da LogP -2.32 TPSA 238.0	3 viol.	✓ Clean	`c1cc(ccc1C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@H](…`
YSC	6HB5	P0AGJ9	485.5 Da LogP -2.90 TPSA 229.3	2 viol.	✓ Clean	`c1cc(ccc1C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@H](…`

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
CHEMBL4208126	P0AGJ9	7.52	508.5 Da LogP -1.71 TPSA 225.1	3 viol.	✓ Clean	`Nc1nccc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)NC(=O)[C…`
YSU	P0AGJ9	7.36	486.5 Da LogP -3.19 TPSA 223.3	2 viol.	✓ Clean	`c1cc(ccc1C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@H](…`
CHEMBL1163069	P0AGJ9	—	459.5 Da LogP -2.22 TPSA 217.8	1 viol.	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H…`
CHEMBL3265242	P0AGJ9	—	435.5 Da LogP -2.80 TPSA 209.1	1 viol.	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H…`
CHEMBL3265243	P0AGJ9	—	436.4 Da LogP -3.09 TPSA 203.0	1 viol.	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H…`
CHEMBL4467328	P0AGJ9	—	436.4 Da LogP -3.09 TPSA 203.0	1 viol.	✓ Clean	`CC(C)C[C@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2…`
HQ5	P0AGJ9	—	435.5 Da LogP -2.80 TPSA 209.1	1 viol.	✓ Clean	`CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H…`
LSS	P0AGJ9	—	459.5 Da LogP -2.22 TPSA 217.8	1 viol.	✓ Clean	`CC(C)C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([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
ZINC1083817667	1.000	459.5 Da LogP -2.22 TPSA 217.8	1 viol.	✓ Clean	`CC(C)C[C@@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n…`
ZINC14824920	1.000	261.3 Da LogP -0.18 TPSA 126.9	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(OS(=O)(=O)O)cc1)C(=O)O`
ZINC1575	1.000	307.1 Da LogP 0.95 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(O)c(I)c1)C(=O)O`
ZINC2556660	1.000	261.3 Da LogP -0.18 TPSA 126.9	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(OS(=O)(=O)O)cc1)C(=O)O`
ZINC391106	1.000	307.1 Da LogP 0.95 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(O)c(I)c1)C(=O)O`
ZINC936069043	1.000	459.5 Da LogP -2.22 TPSA 217.8	1 viol.	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)NS(=O)(=O)OC[C@@H]1O[C…`
ZINC936069053	1.000	459.5 Da LogP -2.22 TPSA 217.8	1 viol.	✓ Clean	`CC(C)C[C@@H](N)C(=O)NS(=O)(=O)OC[C@@H]1O[C@H](n…`
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`
ZINC168710640	0.779	474.5 Da LogP -4.00 TPSA 260.9	2 viol.	✓ Clean	`NC(=O)CC[C@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[C@@H](…`
ZINC168710738	0.779	474.5 Da LogP -4.00 TPSA 260.9	2 viol.	✓ Clean	`NC(=O)CC[C@H](N)C(=O)NS(=O)(=O)OC[C@H]1O[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…`
ZINC13488353	0.735	459.5 Da LogP -1.38 TPSA 221.3	1 viol.	✓ Clean	`CC[C@H](C)[C@H](N)/C(O)=N/S(=O)(=O)OC[C@H]1O[C@…`
ZINC14967098	0.727	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC218033334	0.727	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC218033425	0.727	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC218033503	0.727	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`NCC(=O)NS(=O)(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc…`
ZINC33821383	0.725	459.5 Da LogP -1.38 TPSA 221.3	1 viol.	✓ Clean	`CC(C)C[C@H](N)/C(O)=N/S(=O)(=O)OC[C@H]1O[C@@H](…`
ZINC6092925	0.718	399.2 Da LogP 2.74 TPSA 92.8	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(Oc2ccc(O)c(I)c2)cc1)C(=O)O`
ZINC2512061	0.706	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)…`
ZINC6091882	0.706	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…`
ZINC6091894	0.706	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)…`
ZINC13354682	0.703	321.1 Da LogP 1.04 TPSA 72.5	✓ Ro5	✓ Clean	`COC(=O)[C@H](N)Cc1ccc(O)c(I)c1`
ZINC13354686	0.703	321.1 Da LogP 1.04 TPSA 72.5	✓ Ro5	✓ Clean	`COC(=O)[C@@H](N)Cc1ccc(O)c(I)c1`
ZINC202880439	0.703	320.1 Da LogP 0.61 TPSA 75.4	✓ Ro5	✓ Clean	`CNC(=O)[C@H](N)Cc1ccc(O)c(I)c1`
ZINC202880453	0.703	320.1 Da LogP 0.61 TPSA 75.4	✓ Ro5	✓ Clean	`CNC(=O)[C@@H](N)Cc1ccc(O)c(I)c1`
ZINC238594226	0.694	309.1 Da LogP 1.38 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(F)c(I)c1)C(=O)O`
ZINC238609587	0.694	325.5 Da LogP 1.90 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(Cl)c(I)c1)C(=O)O`
ZINC238611106	0.694	309.1 Da LogP 1.38 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(F)c(I)c1)C(=O)O`
ZINC32333	0.690	244.1 Da LogP 1.40 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(Br)cc1)C(=O)O`
ZINC32334	0.690	244.1 Da LogP 1.40 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(Br)cc1)C(=O)O`
ZINC3679925	0.690	291.1 Da LogP 1.25 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(I)cc1)C(=O)O`
ZINC391104	0.690	291.1 Da LogP 1.25 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(I)cc1)C(=O)O`
ZINC4202286	0.690	209.2 Da LogP 0.34 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(C(=O)O)cc1)C(=O)O`
ZINC4202287	0.690	209.2 Da LogP 0.34 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(C(=O)O)cc1)C(=O)O`
ZINC6092920	0.690	223.2 Da LogP 0.27 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(CC(=O)O)cc1)C(=O)O`
ZINC6506146	0.690	223.2 Da LogP 0.27 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(CC(=O)O)cc1)C(=O)O`
ZINC34319489	0.688	231.3 Da LogP 1.50 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc2cc(O)ccc2c1)C(=O)O`
ZINC34319490	0.688	231.3 Da LogP 1.50 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc2cc(O)ccc2c1)C(=O)O`
ZINC3861723	0.676	433.0 Da LogP 1.56 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1cc(I)c(O)c(I)c1)C(=O)O`
ZINC3875424	0.676	433.0 Da LogP 1.56 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1cc(I)c(O)c(I)c1)C(=O)O`
ZINC113264413	0.667	317.4 Da LogP 3.98 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccc(-c3ccccc3)cc2)cc1)C(=O)O`
ZINC12405780	0.667	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@@H]…`
ZINC12502832	0.667	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@@H]…`
ZINC14982778	0.667	207.2 Da LogP 0.84 TPSA 80.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C[C@@H](N)C(=O)O)cc1`
ZINC14982780	0.667	207.2 Da LogP 0.84 TPSA 80.4	✓ Ro5	✓ Clean	`CC(=O)c1ccc(C[C@H](N)C(=O)O)cc1`
ZINC1569734	0.667	238.2 Da LogP -0.54 TPSA 112.6	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(O)cc1)C(=O)NCC(=O)O`
ZINC2244337	0.667	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(-c2ccccc2)cc1)C(=O)O`
ZINC2244338	0.667	241.3 Da LogP 2.31 TPSA 63.3	✓ Ro5	✓ Clean	`N[C@H](Cc1ccc(-c2ccccc2)cc1)C(=O)O`
ZINC2505456	0.667	210.2 Da LogP 0.72 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)C(Cc1ccc(O)cc1)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.