Protein profile

PA2612

serine--tRNA ligase

Genome: NC_002516.2

Gene: serS PA2612 Structure source: Experimental + AlphaFold UniProt Q9I0M6

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Amino acids 426

Annotations 9

Features 35

PDB binders 4

Druggability 0.503

Overview

Basic information about this protein and its source genome.

Accession: PA2612
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: serS PA2612
Status: annotated
Amino acids: 426
Structure source: Experimental + AlphaFold

6.1.1.11

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0004828 Catalysis of the reaction: ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser). Also catalyzes the formation of L-seryl-tRNA(Sec) from tRNA(Sec), the special tRNA for selenocysteine. GO:0016260 The chemical reactions and pathways resulting in the formation of L-selenocysteine, an essential component of glutathione peroxidase and some other proteins. GO:0006434 The process of coupling serine to seryl-tRNA, catalyzed by seryl-tRNA synthetase. The seryl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a serine-accetping tRNA. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 37.903
Human E-value: 1.7599999999999997e-23
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 0.503

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

6.1.1.11

Gene Ontology (GO)

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0004828 Catalysis of the reaction: ATP + L-serine + tRNA(Ser) = AMP + diphosphate + L-seryl-tRNA(Ser). Also catalyzes the formation of L-seryl-tRNA(Sec) from tRNA(Sec), the special tRNA for selenocysteine.
GO:0016260 The chemical reactions and pathways resulting in the formation of L-selenocysteine, an essential component of glutathione peroxidase and some other proteins.
GO:0006434 The process of coupling serine to seryl-tRNA, catalyzed by seryl-tRNA synthetase. The seryl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a serine-accetping tRNA.
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: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.

35 records

Show feature table

Start	End	DB	Term	Name
138	412	ProSiteProfiles	PS50862	Aminoacyl-transfer RNA synthetases class-II family profile.
138	412	InterPro	IPR006195	Aminoacyl-tRNA synthetase, class II
218	402	Pfam	PF00587	tRNA synthetase class II core domain (G, H, P, S and T)
218	402	InterPro	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)
318	331	PRINTS	PR00981	Seryl-tRNA synthetase signature
318	331	InterPro	IPR002317	Serine-tRNA ligase, type1
266	278	PRINTS	PR00981	Seryl-tRNA synthetase signature
266	278	InterPro	IPR002317	Serine-tRNA ligase, type1
278	291	PRINTS	PR00981	Seryl-tRNA synthetase signature
278	291	InterPro	IPR002317	Serine-tRNA ligase, type1
353	369	PRINTS	PR00981	Seryl-tRNA synthetase signature
353	369	InterPro	IPR002317	Serine-tRNA ligase, type1
335	351	PRINTS	PR00981	Seryl-tRNA synthetase signature
335	351	InterPro	IPR002317	Serine-tRNA ligase, type1
1	112	SUPERFAMILY	SSF46589	tRNA-binding arm
1	112	InterPro	IPR010978	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm
1	426	PIRSF	PIRSF001529	Ser-tRNA_ligase
1	426	InterPro	IPR002317	Serine-tRNA ligase, type1
1	107	Pfam	PF02403	Seryl-tRNA synthetase N-terminal domain
1	107	InterPro	IPR015866	Serine-tRNA synthetase, type1, N-terminal
30	50	Coils	Coil	Coil
116	423	SUPERFAMILY	SSF55681	Class II aaRS and biotin synthetases
116	423	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
119	419	CDD	cd00770	SerRS_core
119	419	InterPro	IPR033729	Serine-tRNA ligase catalytic core domain
1	424	Hamap	MF_00176	Serine--tRNA ligase [serS].
1	424	InterPro	IPR002317	Serine-tRNA ligase, type1
105	425	Gene3D	G3DSA:3.30.930.10	Bira Bifunctional Protein; Domain 2
105	425	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
1	425	PANTHER	PTHR43697	SERYL-TRNA SYNTHETASE
75	95	Coils	Coil	Coil
1	104	Gene3D	G3DSA:1.10.287.40	-
1	104	InterPro	IPR042103	Serine-tRNA synthetase, type1, N-terminal domain superfamily
1	419	NCBIfam	TIGR00414	serine--tRNA ligase
1	419	InterPro	IPR002317	Serine-tRNA ligase, type1

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

3 + 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 6HDZ	X-ray	2.06 Å	A,B	100.0% 1-426	PDBe RCSB PDBj File	Viewing
PDB 6HE3	X-ray	2.16 Å	A,B	100.0% 1-426	PDBe RCSB PDBj File	Loaded
PDB 6HE1	X-ray	2.22 Å	A,B	100.0% 1-426	PDBe RCSB PDBj File	Loaded
AlphaFold PA2612	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				0.503
4				0.209

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	17.6	0.805
2	4.65	0.202
3	2.71	0.081
4	1.98	0.042

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				0.594
4				0.252
3				0.222

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.

58 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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
FZK	6HDZ 2.06 Å Open crystal	410.4 Da LogP -5.15 TPSA 223.3	2 viol.	✓ Clean	`C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`
FZQ	6HE3 2.16 Å Open crystal	409.4 Da LogP -4.86 TPSA 229.3	2 viol.	✓ Clean	`C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`
FZT	6HE1 2.22 Å Open crystal	424.4 Da LogP -5.14 TPSA 212.4	1 viol.	✓ Clean	`CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…`

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
SSA	6R1N	P95689	433.4 Da LogP -4.28 TPSA 238.0	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`

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
CHEMBL4529844	P95689	6.58	467.8 Da LogP -3.62 TPSA 238.0	2 viol.	✓ Clean	`Nc1nc(Cl)nc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)NC(=…`
JPE	P0A8L1	6.54	510.5 Da LogP -3.21 TPSA 250.9	3 viol.	✓ Clean	`c1cc(cnc1)c2nc(c3c(n2)n(cn3)[C@H]4[C@@H]([C@@H]…`
CHEMBL4467050	P95689	6.42	559.3 Da LogP -3.67 TPSA 238.0	3 viol.	✓ Clean	`Nc1nc(I)nc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)NC(=O…`
CHEMBL4208640	P0A8L1	6.28	432.4 Da LogP -3.67 TPSA 225.1	2 viol.	✓ Clean	`Nc1nccc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)NC(=O)[C…`

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
ZINC61947659	0.661	323.3 Da LogP -2.74 TPSA 174.2	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COS(=O)(=O)O)[C@@H](O)[C@H…`
ZINC35929589	0.597	313.3 Da LogP -1.36 TPSA 136.9	✓ Ro5	✓ Clean	`CC(C)C(=O)OC[C@H]1O[C@@H](n2ccc(N)nc2=O)[C@H](O…`
ZINC231393132	0.593	287.2 Da LogP -2.75 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)OC[C@@H]1O[C@H](n2ccc(=O)[nH]c2=O)[C@H](O…`
ZINC231393162	0.593	287.2 Da LogP -2.75 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)OC[C@@H]1O[C@H](n2ccc(=O)[nH]c2=O)[C@@H](…`
ZINC5104172	0.593	287.2 Da LogP -2.75 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)OC[C@@H]1O[C@H](n2ccc(=O)[nH]c2=O)[C@H](O…`
ZINC5104173	0.593	287.2 Da LogP -2.75 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)OC[C@@H]1O[C@@H](n2ccc(=O)[nH]c2=O)[C@H](…`
ZINC5104174	0.593	287.2 Da LogP -2.75 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)OC[C@@H]1O[C@H](n2ccc(=O)[nH]c2=O)[C@@H](…`
ZINC5104175	0.593	287.2 Da LogP -2.75 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)OC[C@@H]1O[C@@H](n2ccc(=O)[nH]c2=O)[C@@H]…`
ZINC5139067	0.593	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CS)[C@@H](O)[C@H]1O`
ZINC1532524	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC16546001	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC1785780	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@@H…`
ZINC1785781	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@@H]…`
ZINC38219836	0.590	314.3 Da LogP -1.64 TPSA 130.8	✓ Ro5	✓ Clean	`CC(C)C(=O)OC[C@H]1O[C@@H](n2ccc(=O)[nH]c2=O)[C@…`
ZINC3861744	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H]…`
ZINC3869480	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H]…`
ZINC3869481	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC3869482	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@H…`
ZINC3869483	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC3954230	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC8613159	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC8952080	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC9007749	0.590	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC100935907	0.583	286.2 Da LogP -2.28 TPSA 130.8	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@H](n2ccc(=O)[nH]c2=O)[C@H](O…`
ZINC13150474	0.583	286.2 Da LogP -2.28 TPSA 130.8	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@H](n2ccc(=O)[nH]c2=O)[C@@H](…`
ZINC2047403	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1O`
ZINC2047673	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC205014459	0.583	286.2 Da LogP -2.28 TPSA 130.8	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@H](n2ccc(=O)[nH]c2=O)[C@@H](…`
ZINC205014473	0.583	286.2 Da LogP -2.28 TPSA 130.8	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@H](n2ccc(=O)[nH]c2=O)[C@H](O…`
ZINC2169830	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC3201876	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC3201878	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC3830178	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3830179	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3978047	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC3978048	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC3978049	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC4048240	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC8580514	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC895113	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC896706	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC970363	0.583	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC4188096	0.574	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188103	0.574	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC4188112	0.574	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188116	0.574	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC12336758	0.569	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c(=O)n1`
ZINC16969357	0.569	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC3830623	0.569	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c(=O)n1`
ZINC3830624	0.569	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c(=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.