Protein profile

HT085_RS00335

tyrosine--tRNA ligase

Genome: NZ_AP023069.1

Gene: tyrS NCTC11421_02832 TUM19854C_00560 Structure source: AlphaFold UniProt A0A1D3GBP6

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Amino acids 431

Annotations 7

Features 32

PDB binders 8

Overview

Basic information about this protein and its source genome.

Accession: HT085_RS00335
Assembly: Neisseria gonorrhoeae strain TUM19854 chromosome, complete genome
Gene: tyrS NCTC11421_02832 TUM19854C_00560
Status: annotated
Amino acids: 431
Structure source: AlphaFold

6.1.1.1

GO:0004831 Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H+. 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:0003723 Binding to an RNA molecule or a portion thereof. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0042803 Binding to an identical protein to form a homodimer.

Target profile

Computed evidence for target prioritization.

Human off-target: 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 Medium

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

6.1.1.1

Gene Ontology (GO)

GO:0004831 Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H+.
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:0003723 Binding to an RNA molecule or a portion thereof.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0042803 Binding to an identical protein to form a homodimer.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records

Show feature table

Start	End	DB	Term	Name
359	388	CDD	cd00165	S4
1	430	Hamap	MF_02006	Tyrosine--tRNA ligase [tyrS].
1	430	InterPro	IPR024107	Tyrosine-tRNA ligase, bacterial-type, type 1
224	327	FunFam	G3DSA:1.10.240.10:FF:000001	Tyrosine--tRNA ligase
39	49	ProSitePatterns	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.
39	49	InterPro	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site
324	430	SUPERFAMILY	SSF55174	Alpha-L RNA-binding motif
1	223	Gene3D	G3DSA:3.40.50.620	HUPs
1	223	InterPro	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold
2	324	SUPERFAMILY	SSF52374	Nucleotidylyl transferase
2	429	PANTHER	PTHR11766	TYROSYL-TRNA SYNTHETASE
2	429	InterPro	IPR024088	Tyrosine-tRNA ligase, bacterial-type
331	431	FunFam	G3DSA:3.10.290.10:FF:000027	Tyrosine--tRNA ligase
4	430	NCBIfam	TIGR00234	tyrosine--tRNA ligase
4	430	InterPro	IPR002307	Tyrosine-tRNA ligase
224	330	Gene3D	G3DSA:1.10.240.10	-
331	431	Gene3D	G3DSA:3.10.290.10	-
331	431	InterPro	IPR036986	RNA-binding S4 domain superfamily
1	223	FunFam	G3DSA:3.40.50.620:FF:000008	Tyrosine--tRNA ligase
28	324	Pfam	PF00579	tRNA synthetases class I (W and Y)
28	324	InterPro	IPR002305	Aminoacyl-tRNA synthetase, class Ic
31	306	CDD	cd00805	TyrRS_core
31	306	InterPro	IPR002307	Tyrosine-tRNA ligase
353	422	ProSiteProfiles	PS50889	S4 RNA-binding domain profile.
217	229	PRINTS	PR01040	Tyrosyl-tRNA synthetase signature
217	229	InterPro	IPR002307	Tyrosine-tRNA ligase
184	206	PRINTS	PR01040	Tyrosyl-tRNA synthetase signature
184	206	InterPro	IPR002307	Tyrosine-tRNA ligase
43	65	PRINTS	PR01040	Tyrosyl-tRNA synthetase signature
43	65	InterPro	IPR002307	Tyrosine-tRNA ligase
163	178	PRINTS	PR01040	Tyrosyl-tRNA synthetase signature
163	178	InterPro	IPR002307	Tyrosine-tRNA ligase

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 HT085_RS00335	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
4				0.535

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	Score	Probability
1	28.75	0.891
2	5.34	0.207
3	1.54	0.019
4	1.4	0.015
5	1.32	0.012

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](…`
YSU	6HB6	P0AGJ9	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](…`

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…`
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…`
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](…`
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`
ZINC2512061	0.677	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	0.677	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	0.677	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)…`
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`
ZINC113264415	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`
ZINC2575475	0.667	238.2 Da LogP -0.54 TPSA 112.6	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(O)cc1)C(=O)NCC(=O)O`
ZINC2575618	0.667	208.2 Da LogP -0.26 TPSA 106.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc(C[C@H](N)C(=O)O)cc1`
ZINC4241956	0.667	208.2 Da LogP -0.26 TPSA 106.4	✓ Ro5	✓ Clean	`NC(=O)c1ccc(C[C@@H](N)C(=O)O)cc1`
ZINC79460727	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](…`
ZINC79460732	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](…`
ZINC20268092	0.654	230.1 Da LogP 1.31 TPSA 46.2	✓ Ro5	✓ Clean	`N[C@@H](CO)Cc1ccc(Br)cc1`
ZINC20268094	0.654	230.1 Da LogP 1.31 TPSA 46.2	✓ Ro5	✓ Clean	`N[C@H](CO)Cc1ccc(Br)cc1`
ZINC44466880	0.654	277.1 Da LogP 1.15 TPSA 46.2	✓ Ro5	✓ Clean	`N[C@H](CO)Cc1ccc(I)cc1`
ZINC44466883	0.654	277.1 Da LogP 1.15 TPSA 46.2	✓ Ro5	✓ Clean	`N[C@@H](CO)Cc1ccc(I)cc1`
ZINC2004481	0.647	344.4 Da LogP 0.78 TPSA 132.9	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccc(O)cc1)C(=O)N[C@@H](Cc1ccc(O)cc1)…`
ZINC2392306	0.645	221.3 Da LogP 1.94 TPSA 63.3	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc(C[C@@H](N)C(=O)O)cc1`
ZINC3679865	0.645	207.3 Da LogP 1.76 TPSA 63.3	✓ Ro5	✓ Clean	`CC(C)c1ccc(C[C@@H](N)C(=O)O)cc1`
ZINC44284738	0.645	255.3 Da LogP 2.62 TPSA 63.3	✓ Ro5	✓ Clean	`Cc1ccc(-c2ccc(C[C@H](N)C(=O)O)cc2)cc1`

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.