Protein profile

KP13_00709

Tryptophanyl-tRNA synthetase

Genome: KpKP13

Gene: trpS AHE42327.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GU65

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Amino acids 334

Annotations 8

Features 25

PDB binders 8

Druggability 0.401

Overview

Basic information about this protein and its source genome.

Accession: KP13_00709
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: trpS AHE42327.1
Status: annotated
Amino acids: 334
Structure source: AlphaFold + ColabFold

6.1.1.2

GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP. GO:0006436 The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-tRNA synthetase. The tryptophanyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tryptophan-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification. 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:0004830 Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp). 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 (%): 42.296
Human E-value: 5.96e-87
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 95.21
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 94.28

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 0.401

Structure A0A0H3GU65

Pocket Pocket 26

P2Rank 0.851

Structure A0A0H3GU65

Pocket Pocket 1

ColabFold model

FPocket 0.369 · Pocket 1

P2Rank 0.88 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 1492 / 4744 genomes with a hit

Normalized 0.315

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

6.1.1.2

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:0006436 The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-tRNA synthetase. The tryptophanyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tryptophan-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
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:0004830 Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp).
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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records

Show feature table

Start	End	DB	Term	Name
142	163	PRINTS	PR01039	Tryptophanyl-tRNA synthetase signature
142	163	InterPro	IPR002306	Tryptophan-tRNA ligase
195	205	PRINTS	PR01039	Tryptophanyl-tRNA synthetase signature
195	205	InterPro	IPR002306	Tryptophan-tRNA ligase
16	32	PRINTS	PR01039	Tryptophanyl-tRNA synthetase signature
16	32	InterPro	IPR002306	Tryptophan-tRNA ligase
66	85	PRINTS	PR01039	Tryptophanyl-tRNA synthetase signature
66	85	InterPro	IPR002306	Tryptophan-tRNA ligase
3	285	Pfam	PF00579	tRNA synthetases class I (W and Y)
3	285	InterPro	IPR002305	Aminoacyl-tRNA synthetase, class Ic
186	298	FunFam	G3DSA:1.10.240.10:FF:000002	Tryptophan--tRNA ligase
6	212	FunFam	G3DSA:3.40.50.620:FF:000024	Tryptophan--tRNA ligase
5	284	CDD	cd00806	TrpRS_core
5	284	InterPro	IPR002306	Tryptophan-tRNA ligase
3	331	Hamap	MF_00140_B	Tryptophan--tRNA ligase [trpS].
3	331	InterPro	IPR024109	Tryptophan-tRNA ligase, bacterial-type
6	329	Gene3D	G3DSA:3.40.50.620	HUPs
6	329	InterPro	IPR014729	Rossmann-like alpha/beta/alpha sandwich fold
12	21	ProSitePatterns	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.
12	21	InterPro	IPR001412	Aminoacyl-tRNA synthetase, class I, conserved site
3	330	NCBIfam	TIGR00233	tryptophan--tRNA ligase
3	330	InterPro	IPR002306	Tryptophan-tRNA ligase
3	330	PANTHER	PTHR43766	TRYPTOPHAN--TRNA LIGASE, MITOCHONDRIAL
5	330	SUPERFAMILY	SSF52374	Nucleotidylyl transferase
186	298	Gene3D	G3DSA:1.10.240.10	-

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_A0A0H3GU65	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00709	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
26				0.401
2				0.262

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	11.88	0.629
2	2.83	0.088
3	2.23	0.055
4	1.92	0.039
5	1.3	0.014

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				0.369

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	8.67	0.464
2	8.32	0.443
3	1.44	0.019
4	1.1	0.008

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
5BX	5DK4	P00953	257.3 Da LogP 1.77 TPSA 66.5	✓ Ro5	✓ Clean	`C[C@H](c1c[nH]c2c1cccc2)[C@H]3C(=O)N=C(O3)NC`
9E0	7CMS	P00953	233.3 Da LogP 2.83 TPSA 53.1	✓ Ro5	✓ Clean	`C[C@H]1c2c[nH]c3c2c(ccc3)S[C@H]1C(=O)O`
ANL	2OV4	P00953	93.1 Da LogP 1.27 TPSA 26.0	✓ Ro5	✓ Clean	`c1ccc(cc1)N`
AQP	2OV4	P00953	587.2 Da LogP -1.51 TPSA 325.7	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
LTN	1MAU	P00953	203.2 Da LogP 0.52 TPSA 84.9	✓ Ro5	✓ Clean	`c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)N)N`
NH4	1I6K	P00953	18.0 Da LogP 0.38 TPSA 36.5	✓ Ro5	✓ Clean	`[NH4+]`
TYM	1I6K	P00953	533.4 Da LogP -0.26 TPSA 233.9	3 viol.	✓ Clean	`c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O[P@](=O)(O)OC…`
WSA	2YY5	P75510	532.5 Da LogP -1.54 TPSA 233.6	3 viol.	✓ Clean	`c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)NS(=O)(=O)OC[C…`

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
ZINC13508004	1.000	257.3 Da LogP 1.77 TPSA 66.5	✓ Ro5	✓ Clean	`CNC1=NC(=O)[C@@H]([C@@H](C)c2c[nH]c3ccccc23)O1`
ZINC13508006	1.000	257.3 Da LogP 1.77 TPSA 66.5	✓ Ro5	✓ Clean	`CNC1=NC(=O)[C@H]([C@@H](C)c2c[nH]c3ccccc23)O1`
ZINC3964188	1.000	257.3 Da LogP 1.77 TPSA 66.5	✓ Ro5	✓ Clean	`CNC1=NC(=O)[C@H]([C@H](C)c2c[nH]c3ccccc23)O1`
ZINC83315	1.000	204.2 Da LogP 1.12 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@@H](Cc1c[nH]c2ccccc12)C(=O)O`
ZINC83317	1.000	204.2 Da LogP 1.12 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@H](Cc1c[nH]c2ccccc12)C(=O)O`
ZINC9049	1.000	257.3 Da LogP 1.77 TPSA 66.5	✓ Ro5	✓ Clean	`CNC1=NC(=O)[C@@H]([C@H](C)c2c[nH]c3ccccc23)O1`
ZINC12360002	0.980	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	0.980	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	0.980	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	0.980	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	0.980	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	0.980	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	0.980	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586019	0.980	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	0.980	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC8586021	0.980	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	0.980	427.2 Da LogP -1.75 TPSA 232.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC13518964	0.830	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC1532515	0.830	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	0.830	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC1842158	0.830	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	0.830	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@H](…`
ZINC2126310	0.830	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201891	0.830	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COP(=O)(O)O)[C@@H]…`
ZINC3201893	0.830	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.830	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3860156	0.830	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.830	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	0.830	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	0.830	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC34718738	0.786	444.3 Da LogP -1.04 TPSA 206.6	2 viol.	✓ Clean	`O=P(O)(O)O[P@](=O)(O)OC[C@@H]1O[C@H](n2cnc3c(S)…`
ZINC34718739	0.786	444.3 Da LogP -1.04 TPSA 206.6	2 viol.	✓ Clean	`O=P(O)(O)O[P@](=O)(O)OC[C@@H]1O[C@@H](n2cnc3c(S…`
ZINC34718740	0.786	444.3 Da LogP -1.04 TPSA 206.6	2 viol.	✓ Clean	`O=P(O)(O)O[P@](=O)(O)OC[C@@H]1O[C@H](n2cnc3c(S)…`
ZINC34718741	0.786	444.3 Da LogP -1.04 TPSA 206.6	2 viol.	✓ Clean	`O=P(O)(O)O[P@](=O)(O)OC[C@@H]1O[C@@H](n2cnc3c(S…`
ZINC4096224	0.782	346.2 Da LogP -1.90 TPSA 191.9	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@](N)(=O)O)[C@@…`
ZINC4899521	0.778	203.2 Da LogP 0.52 TPSA 84.9	✓ Ro5	✓ Clean	`NC(=O)[C@H](N)Cc1c[nH]c2ccccc12`
ZINC57505	0.778	203.2 Da LogP 0.52 TPSA 84.9	✓ Ro5	✓ Clean	`NC(=O)[C@@H](N)Cc1c[nH]c2ccccc12`
ZINC12503850	0.776	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	0.776	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	0.776	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	0.776	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	0.764	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	0.764	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	0.764	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.764	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC2566035	0.757	218.3 Da LogP 1.51 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@@H](CCc1c[nH]c2ccccc12)C(=O)O`
ZINC6864822	0.757	218.3 Da LogP 1.51 TPSA 79.1	✓ Ro5	✓ Clean	`N[C@H](CCc1c[nH]c2ccccc12)C(=O)O`
ZINC31475423	0.750	434.3 Da LogP -2.99 TPSA 238.4	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO[P@@](=O)(O)OC(=O)…`
ZINC31539924	0.747	494.4 Da LogP -0.74 TPSA 218.2	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO[P@@](=O)(O)OC(=O…`
ZINC13434883	0.746	491.2 Da LogP -0.60 TPSA 258.9	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1C[C@@H](O)[C@H](CO[P@@](=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.