Protein profile

PA0903

alanine--tRNA ligase

Genome: NC_002516.2

Gene: alaS PA0903 Structure source: AlphaFold UniProt Q9I553

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Amino acids 874

Annotations 13

Features 48

PDB binders 7

Druggability 0.343

Overview

Basic information about this protein and its source genome.

Accession: PA0903
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: alaS PA0903
Status: annotated
Amino acids: 874
Structure source: AlphaFold

6.1.1.7

GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0004813 Catalysis of the reaction: ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala). GO:0002161 The hydrolysis of an incorrectly aminoacylated tRNA. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0000049 Binding to a transfer RNA. GO:0008270 Binding to a zinc ion (Zn).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 56.818
Human E-value: 8.25e-11
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 0.343

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 12 GO

Enzyme Commission (EC)

6.1.1.7

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:0004813 Catalysis of the reaction: ATP + L-alanine + tRNA(Ala) = AMP + diphosphate + L-alanyl-tRNA(Ala).
GO:0002161 The hydrolysis of an incorrectly aminoacylated tRNA.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
GO:0000049 Binding to a transfer RNA.
GO:0008270 Binding to a zinc ion (Zn).
GO:0006419 The process of coupling alanine to alanyl-tRNA, catalyzed by alanyl-tRNA synthetase. The alanyl-tRNA synthetase is a class-II synthetases. The activated amino acid is transferred to the 3'-OH group of an alanine accetping tRNA.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
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:0003676 Binding to a nucleic acid.
GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
GO:0043039 The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is 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, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.

Sequence Features

Domain/signature hits from InterPro and related databases.

48 records

Show feature table

Start	End	DB	Term	Name
763	871	Gene3D	G3DSA:3.10.310.40	-
450	550	FunFam	G3DSA:2.40.30.130:FF:000001	Alanine--tRNA ligase
622	676	FunFam	G3DSA:3.30.54.20:FF:000001	Alanine--tRNA ligase
366	386	Coils	Coil	Coil
254	452	SUPERFAMILY	SSF101353	Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)
254	452	InterPro	IPR018162	Alanine-tRNA ligase, class IIc, anti-codon-binding domain superfamily
207	218	PRINTS	PR00980	Alanyl-tRNA synthetase signature
207	218	InterPro	IPR002318	Alanine-tRNA ligase, class IIc
234	247	PRINTS	PR00980	Alanyl-tRNA synthetase signature
234	247	InterPro	IPR002318	Alanine-tRNA ligase, class IIc
304	317	PRINTS	PR00980	Alanyl-tRNA synthetase signature
304	317	InterPro	IPR002318	Alanine-tRNA ligase, class IIc
74	85	PRINTS	PR00980	Alanyl-tRNA synthetase signature
74	85	InterPro	IPR002318	Alanine-tRNA ligase, class IIc
280	296	PRINTS	PR00980	Alanyl-tRNA synthetase signature
280	296	InterPro	IPR002318	Alanine-tRNA ligase, class IIc
3	249	CDD	cd00673	AlaRS_core
763	870	FunFam	G3DSA:3.10.310.40:FF:000001	Alanine--tRNA ligase
551	710	FunFam	G3DSA:3.30.980.10:FF:000004	Alanine--tRNA ligase, cytoplasmic
706	758	Coils	Coil	Coil
651	695	SMART	SM00863	tRNA_SAD_4
651	695	InterPro	IPR012947	Threonyl/alanyl tRNA synthetase, SAD
5	853	NCBIfam	TIGR00344	alanine--tRNA ligase
5	853	InterPro	IPR002318	Alanine-tRNA ligase, class IIc
622	676	Gene3D	G3DSA:3.30.54.20	-
2	253	SUPERFAMILY	SSF55681	Class II aaRS and biotin synthetases
2	253	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
550	706	SUPERFAMILY	SSF55186	ThrRS/AlaRS common domain
550	706	InterPro	IPR018163	Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily
607	627	Coils	Coil	Coil
732	870	Pfam	PF02272	DHHA1 domain
732	870	InterPro	IPR003156	DHHA1 domain
1	874	Hamap	MF_00036_B	Alanine--tRNA ligase [alaS].
1	874	InterPro	IPR023033	Alanine-tRNA ligase, eukaryota/bacteria
452	550	SUPERFAMILY	SSF50447	Translation proteins
452	550	InterPro	IPR009000	Translation protein, beta-barrel domain superfamily
1	250	Gene3D	G3DSA:3.30.930.10	Bira Bifunctional Protein; Domain 2
1	250	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
467	550	Gene3D	G3DSA:2.40.30.130	-
1	250	FunFam	G3DSA:3.30.930.10:FF:000004	Alanine--tRNA ligase
699	761	Gene3D	G3DSA:6.10.250.550	-
651	695	Pfam	PF07973	Threonyl and Alanyl tRNA synthetase second additional domain
1	708	ProSiteProfiles	PS50860	Alanyl-transfer RNA synthetases family profile.
1	708	InterPro	IPR018165	Alanyl-tRNA synthetase, class IIc, core domain
1	871	PANTHER	PTHR11777	ALANYL-TRNA SYNTHETASE
5	552	Pfam	PF01411	tRNA synthetases class II (A)
5	552	InterPro	IPR018164	Alanyl-tRNA synthetase, class IIc, N-terminal
561	697	Gene3D	G3DSA:3.30.980.10	-

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 PA0903	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
3				0.343

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.

57 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
5AL	3HXY	P00957	418.3 Da LogP -1.96 TPSA 218.2	1 viol.	✓ Clean	`C[C@@H](C(=O)O[P@](=O)(O)OC[C@@H]1[C@H]([C@H]([…`
A5A	2ZTG	O28029	417.4 Da LogP -3.25 TPSA 217.8	1 viol.	✓ Clean	`C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H]([C@…`
ACP	3HXY	P00957	505.2 Da LogP -1.52 TPSA 269.9	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
G5A	3HY0	P00957	403.4 Da LogP -3.64 TPSA 217.8	1 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
HED	3HXY	P00957	154.3 Da LogP 0.35 TPSA 40.5	✓ Ro5	✓ Clean	`C(CSSCCO)O`
MDN	3HXY	P00957	176.0 Da LogP -0.70 TPSA 115.1	✓ Ro5	✓ Clean	`C(P(=O)(O)O)P(=O)(O)O`
SSA	3HXW	P00957	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).

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
ZINC1083817667	0.841	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	0.841	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	0.841	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…`
ZINC14967098	0.774	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	0.774	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	0.774	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	0.774	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…`
ZINC168710640	0.773	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	0.773	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](…`
ZINC12405780	0.712	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	0.712	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@@H]…`
ZINC79460727	0.712	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	0.712	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@H](…`
ZINC24951137	0.708	417.4 Da LogP -2.41 TPSA 221.3	1 viol.	✓ Clean	`C[C@H](N)/C(O)=N/S(=O)(=O)OC[C@H]1O[C@@H](n2cnc…`
ZINC20101092	0.692	254.0 Da LogP -0.47 TPSA 152.4	✓ Ro5	✓ Clean	`O=P(O)(O)CP(=O)(O)CP(=O)(O)O`
ZINC13547650	0.656	309.3 Da LogP -1.41 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)…`
ZINC4823971	0.656	309.3 Da LogP -1.41 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O…`
ZINC4823975	0.656	309.3 Da LogP -1.41 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](…`
ZINC4823980	0.656	309.3 Da LogP -1.41 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O…`
ZINC4823984	0.656	309.3 Da LogP -1.41 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](…`
ZINC13488353	0.652	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@…`
ZINC33821383	0.643	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](…`
ZINC1574270	0.642	421.4 Da LogP -0.26 TPSA 162.7	1 viol.	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@@H]2O[C@H](n3cnc4c(N)ncnc4…`
ZINC3861767	0.642	421.4 Da LogP -0.26 TPSA 162.7	1 viol.	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@H]2O[C@@H](n3cnc4c(N)ncnc4…`
ZINC14967079	0.629	461.4 Da LogP -2.95 TPSA 258.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)/N=C(\O)…`
ZINC4824159	0.619	344.4 Da LogP -2.42 TPSA 165.5	✓ Ro5	✓ Clean	`CS(=O)(=O)NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@…`
ZINC4824161	0.619	344.4 Da LogP -2.42 TPSA 165.5	✓ Ro5	✓ Clean	`CS(=O)(=O)NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@…`
ZINC4824165	0.619	344.4 Da LogP -2.42 TPSA 165.5	✓ Ro5	✓ Clean	`CS(=O)(=O)NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@…`
ZINC4824166	0.619	344.4 Da LogP -2.42 TPSA 165.5	✓ Ro5	✓ Clean	`CS(=O)(=O)NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@…`
ZINC12503850	0.612	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141161066	0.612	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC141163786	0.612	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](=O)(O)OS(=O)…`
ZINC4228246	0.612	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC28567519	0.606	466.4 Da LogP -1.00 TPSA 215.5	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)/N=C(\O)…`
ZINC5139067	0.603	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CS)[C@@H](O)[C@H]1O`
ZINC5011204	0.603	295.3 Da LogP -1.80 TPSA 145.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COC=O)[C@@H](O)[C@H…`
ZINC5011205	0.603	295.3 Da LogP -1.80 TPSA 145.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COC=O)[C@@H](O)[C@…`
ZINC5011206	0.603	295.3 Da LogP -1.80 TPSA 145.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COC=O)[C@@H](O)[C@@…`
ZINC5011208	0.603	295.3 Da LogP -1.80 TPSA 145.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COC=O)[C@@H](O)[C@…`
ZINC31260554	0.603	474.5 Da LogP -3.16 TPSA 264.4	2 viol.	✓ Clean	`NC(=O)CC[C@H](N)/C(O)=N/S(=O)(=O)OC[C@H]1O[C@@H…`
ZINC31976683	0.603	474.5 Da LogP -3.16 TPSA 264.4	2 viol.	✓ Clean	`NC(=O)CC[C@H](N)/C(O)=N/S(=O)(=O)OC[C@H]1O[C@@H…`
ZINC105372837	0.594	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC13518964	0.594	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC17107643	0.594	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.594	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC2126310	0.594	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201893	0.594	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.594	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.594	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC8613167	0.594	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](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.