Protein profile

KP13_04211

Seryl-tRNA synthetase

Genome: KpKP13

Gene: AHE45442.1 serS Structure source: Experimental + ColabFold UniProt A6T6Z0|W9BNU9

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Amino acids 430

Annotations 6

Features 37

PDB binders 4

Druggability 0.953

Overview

Basic information about this protein and its source genome.

Accession: KP13_04211
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45442.1 serS
Status: annotated
Amino acids: 430
Structure source: Experimental + ColabFold

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. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. 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: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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 35.013
Human E-value: 1.1699999999999999e-60
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 94.419
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.08

Selected Druggability evidence

PDB experimental structure

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 0.953

Structure 7AP1

Pocket Pocket 3

P2Rank 0.794

Structure 7AP1

Pocket Pocket 1

ColabFold model

FPocket 0.384 · Pocket 3

P2Rank 0.876 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 1346 / 4744 genomes with a hit

Normalized 0.284

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

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: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: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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

37 records

Show feature table

Start	End	DB	Term	Name
1	423	NCBIfam	TIGR00414	serine--tRNA ligase
1	423	InterPro	IPR002317	Serine-tRNA ligase, type1
119	423	CDD	cd00770	SerRS_core
119	423	InterPro	IPR033729	Serine-tRNA ligase catalytic core domain
228	406	Pfam	PF00587	tRNA synthetase class II core domain (G, H, P, S and T)
228	406	InterPro	IPR002314	Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)
1	112	SUPERFAMILY	SSF46589	tRNA-binding arm
1	112	InterPro	IPR010978	Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm
1	430	PIRSF	PIRSF001529	Ser-tRNA_ligase
1	430	InterPro	IPR002317	Serine-tRNA ligase, type1
1	104	FunFam	G3DSA:1.10.287.40:FF:000001	Serine--tRNA ligase
68	102	Coils	Coil	Coil
282	295	PRINTS	PR00981	Seryl-tRNA synthetase signature
282	295	InterPro	IPR002317	Serine-tRNA ligase, type1
322	335	PRINTS	PR00981	Seryl-tRNA synthetase signature
322	335	InterPro	IPR002317	Serine-tRNA ligase, type1
270	282	PRINTS	PR00981	Seryl-tRNA synthetase signature
270	282	InterPro	IPR002317	Serine-tRNA ligase, type1
339	355	PRINTS	PR00981	Seryl-tRNA synthetase signature
339	355	InterPro	IPR002317	Serine-tRNA ligase, type1
357	373	PRINTS	PR00981	Seryl-tRNA synthetase signature
357	373	InterPro	IPR002317	Serine-tRNA ligase, type1
30	50	Coils	Coil	Coil
1	429	PANTHER	PTHR43697	SERYL-TRNA SYNTHETASE
1	107	Pfam	PF02403	Seryl-tRNA synthetase N-terminal domain
1	107	InterPro	IPR015866	Serine-tRNA synthetase, type1, N-terminal
116	424	SUPERFAMILY	SSF55681	Class II aaRS and biotin synthetases
116	424	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
1	104	Gene3D	G3DSA:1.10.287.40	-
1	104	InterPro	IPR042103	Serine-tRNA synthetase, type1, N-terminal domain superfamily
105	430	FunFam	G3DSA:3.30.930.10:FF:000018	Serine--tRNA ligase
105	430	Gene3D	G3DSA:3.30.930.10	Bira Bifunctional Protein; Domain 2
105	430	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
1	428	Hamap	MF_00176	Serine--tRNA ligase [serS].
1	428	InterPro	IPR002317	Serine-tRNA ligase, type1
171	416	ProSiteProfiles	PS50862	Aminoacyl-transfer RNA synthetases class-II family profile.
171	416	InterPro	IPR006195	Aminoacyl-tRNA synthetase, class II

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

1 + 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 7AP1	X-ray	20.00 Å	-	—	PDBe RCSB PDBj File	Viewing
ColabFold KP13_04211	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
3				0.953
1				0.366

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	17.04	0.794
2	4.39	0.185
3	3.86	0.151
4	2.1	0.048
5	1.8	0.034

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				0.384

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	14.91	0.739
2	5.88	0.287
3	2.88	0.091
4	2.44	0.066

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.

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
FZK	6HI0	A6T6Z0	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	6HHZ	A6T6Z0	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	6HHY	A6T6Z0	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)…`
JPE	6R1O	P0A8L1	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]…`

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
SSA	P0A8L1	9.74	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)…`
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…`
CHEMBL4529844	P0A8L1	6.35	467.8 Da LogP -3.62 TPSA 238.0	2 viol.	✓ Clean	`Nc1nc(Cl)nc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)NC(=…`
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
ZINC1083817667	0.828	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	0.828	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	0.815	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	0.815	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](…`
ZINC936069043	0.773	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…`
ZINC14967098	0.762	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	0.762	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	0.762	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	0.762	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…`
ZINC12405780	0.700	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	0.700	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	0.700	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	0.700	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@H](…`
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…`
ZINC31475423	0.657	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=O)…`
ZINC14967079	0.643	461.4 Da LogP -2.95 TPSA 258.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)/N=C(\O)…`
ZINC24951137	0.623	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…`
ZINC13547650	0.619	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	0.619	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	0.619	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	0.619	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	0.619	309.3 Da LogP -1.41 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](…`
ZINC31260554	0.616	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	0.616	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…`
ZINC33821383	0.611	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](…`
ZINC13518964	0.609	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.609	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	0.609	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.609	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	0.609	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.609	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.609	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.609	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.609	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.609	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.609	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	0.609	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	0.609	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC1574270	0.609	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	0.609	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…`
ZINC13488353	0.597	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@…`
ZINC5011204	0.594	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	0.594	295.3 Da LogP -1.80 TPSA 145.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COC=O)[C@@H](O)[C@…`
ZINC5011206	0.594	295.3 Da LogP -1.80 TPSA 145.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COC=O)[C@@H](O)[C@@…`
ZINC5011208	0.594	295.3 Da LogP -1.80 TPSA 145.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COC=O)[C@@H](O)[C@…`
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`
ZINC49014951	0.588	416.4 Da LogP -2.76 TPSA 216.8	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CS(=O)(=O)CC[C@H](N)…`
ZINC49014955	0.588	416.4 Da LogP -2.76 TPSA 216.8	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CS(=O)(=O)CC[C@@H](N…`
ZINC17107643	0.585	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.585	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=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.