Protein profile

KP13_31936

aspartyl-tRNA synthetase

Genome: KpKP13

Gene: aspS AHE43852.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H058

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Amino acids 595

Annotations 10

Features 39

PDB binders 3

Druggability 0.348

Overview

Basic information about this protein and its source genome.

Accession: KP13_31936
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: aspS AHE43852.1
Status: annotated
Amino acids: 595
Structure source: AlphaFold + ColabFold

6.1.1.12

GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0003676 Binding to a nucleic acid. GO:0016874 Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient. 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. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 62.963
Human E-value: 1.23e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 94.369
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 95.64

Selected Druggability evidence

AlphaFold / UniProt model

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 0.348

Structure A0A0H3H058

Pocket Pocket 1

P2Rank 0.903

Structure A0A0H3H058

Pocket Pocket 1

ColabFold model

FPocket 0.579 · Pocket 1

P2Rank 0.905 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 907 / 4744 genomes with a hit

Normalized 0.191

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

6.1.1.12

Gene Ontology (GO)

GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0003676 Binding to a nucleic acid.
GO:0016874 Catalysis of the joining of two molecules, or two groups within a single molecule, using the energy from the hydrolysis of ATP, a similar triphosphate, or a pH gradient.
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.
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
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:0004815 Catalysis of the reaction: ATP + L-aspartate + tRNA(Asp) = AMP + diphosphate + L-aspartyl-tRNA(Asp).
GO:0006422 The process of coupling aspartate to aspartyl-tRNA, catalyzed by aspartyl-tRNA synthetase. The aspartyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of an aspartic acid accetping tRNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

39 records

Show feature table

Start	End	DB	Term	Name
18	102	Pfam	PF01336	OB-fold nucleic acid binding domain
18	102	InterPro	IPR004365	OB-fold nucleic acid binding domain, AA-tRNA synthetase-type
190	202	PRINTS	PR01042	Aspartyl-tRNA synthetase signature
190	202	InterPro	IPR002312	Aspartyl/Asparaginyl-tRNA synthetase, class IIb
518	532	PRINTS	PR01042	Aspartyl-tRNA synthetase signature
518	532	InterPro	IPR002312	Aspartyl/Asparaginyl-tRNA synthetase, class IIb
207	220	PRINTS	PR01042	Aspartyl-tRNA synthetase signature
207	220	InterPro	IPR002312	Aspartyl/Asparaginyl-tRNA synthetase, class IIb
474	490	PRINTS	PR01042	Aspartyl-tRNA synthetase signature
474	490	InterPro	IPR002312	Aspartyl/Asparaginyl-tRNA synthetase, class IIb
1	584	Hamap	MF_00044	Aspartate--tRNA(Asp/Asn) ligase [aspS].
1	584	InterPro	IPR004524	Aspartate-tRNA ligase, type 1
271	420	Gene3D	G3DSA:3.30.1360.30	-
271	420	InterPro	IPR004115	GAD-like domain superfamily
108	584	SUPERFAMILY	SSF55681	Class II aaRS and biotin synthetases
108	584	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
307	406	Pfam	PF02938	GAD domain
307	406	InterPro	IPR029351	GAD domain
1	106	FunFam	G3DSA:2.40.50.140:FF:000080	Aspartate--tRNA ligase
1	585	NCBIfam	TIGR00459	aspartate--tRNA ligase
1	585	InterPro	IPR004524	Aspartate-tRNA ligase, type 1
1	105	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
1	105	InterPro	IPR012340	Nucleic acid-binding, OB-fold
4	560	PANTHER	PTHR22594	ASPARTYL/LYSYL-TRNA SYNTHETASE
1	106	Gene3D	G3DSA:2.40.50.140	-
1	106	InterPro	IPR012340	Nucleic acid-binding, OB-fold
271	420	FunFam	G3DSA:3.30.1360.30:FF:000001	Aspartate--tRNA ligase
118	558	Pfam	PF00152	tRNA synthetases class II (D, K and N)
118	558	InterPro	IPR004364	Aminoacyl-tRNA synthetase, class II (D/K/N)
138	558	CDD	cd00777	AspRS_core
138	558	InterPro	IPR047090	Aspartate-tRNA ligase, type 1, core domain
118	579	Gene3D	G3DSA:3.30.930.10	Bira Bifunctional Protein; Domain 2
118	579	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
138	555	ProSiteProfiles	PS50862	Aminoacyl-transfer RNA synthetases class-II family profile.
138	555	InterPro	IPR006195	Aminoacyl-tRNA synthetase, class II
288	419	SUPERFAMILY	SSF55261	GAD domain-like
288	419	InterPro	IPR004115	GAD-like domain superfamily
2	134	CDD	cd04317	EcAspRS_like_N
2	134	InterPro	IPR047089	Aspartate-tRNA ligase, type 1, anticodon recognition domain

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

0 + 2

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3H058	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_31936	ColabFold	—	—	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				0.348

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	16.01	0.768
2	1.98	0.042
3	1.84	0.036
4	1.21	0.011
5	0.93	0.004

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				0.579

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	19.24	0.836
2	1.84	0.036
3	1.84	0.036
4	1.74	0.031
5	1.45	0.019

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.

55 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
3SY	4RMF	A0QWN3	136.1 Da LogP -2.06 TPSA 80.9	✓ Ro5	✓ Clean	`C(C(CO)(CO)CO)O`
AMO	1C0A	P21889	462.3 Da LogP -2.51 TPSA 255.5	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
BUA	5GRO	P56459	88.1 Da LogP 0.87 TPSA 37.3	✓ Ro5	✓ Clean	`CCCC(=O)O`

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
DSZ	P21889	10.28	461.4 Da LogP -3.79 TPSA 255.1	2 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
CHEMBL4203761	P21889	7.60	460.4 Da LogP -3.19 TPSA 242.2	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
ZINC31475423	0.850	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=O)…`
ZINC1083817667	0.831	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…`
ZINC936069053	0.831	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…`
ZINC168710640	0.791	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	0.791	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](…`
ZINC31539924	0.788	494.4 Da LogP -0.74 TPSA 218.2	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OC(=O…`
ZINC31516918	0.781	446.4 Da LogP -1.33 TPSA 218.2	1 viol.	✓ Clean	`CC(C)[C@H](N)C(=O)O[P@](=O)(O)OC[C@H]1O[C@@H](n…`
ZINC936069043	0.750	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…`
ZINC14967079	0.746	461.4 Da LogP -2.95 TPSA 258.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)/N=C(\O)…`
ZINC14967098	0.738	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	0.738	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	0.738	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	0.738	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…`
ZINC12360002	0.726	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12360703	0.726	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC12503599	0.726	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC16546165	0.726	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@](=O)(O)OP(=O)(…`
ZINC31977053	0.726	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC4806433	0.726	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC53683898	0.726	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.726	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@](=O)(O)OP(=O)…`
ZINC8586020	0.726	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.726	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC8586022	0.726	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC13518964	0.717	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.717	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC1571045	0.717	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.717	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC2046931	0.717	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.717	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.717	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.717	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.717	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.717	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.717	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](COP(=O)(O)O)[C@@H](O…`
ZINC4806442	0.717	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	0.717	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC4096224	0.705	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC12503850	0.703	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	0.703	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	0.703	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	0.703	427.3 Da LogP -2.04 TPSA 229.4	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OS(=O…`
ZINC105372833	0.689	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC105372837	0.689	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC17107643	0.689	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.689	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC12405780	0.677	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	0.677	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	0.677	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	0.677	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@H](…`

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.