Protein profile

KP13_00246

Glycyl-tRNA synthetase alpha

Genome: KpKP13

Gene: AHE42158.1 glyQ Structure source: AlphaFold + ColabFold UniProt A0A0H3GUM8

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Amino acids 303

Annotations 7

Features 31

PDB binders 2

Druggability 0.376

Overview

Basic information about this protein and its source genome.

Accession: KP13_00246
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42158.1 glyQ
Status: annotated
Amino acids: 303
Structure source: AlphaFold + ColabFold

6.1.1.14

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0004820 Catalysis of the reaction: ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly). GO:0006426 The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-tRNA synthetase. The glycyll-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a glycine-accepting tRNA. 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 99.34
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 97.13

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 0.376

Structure A0A0H3GUM8

Pocket Pocket 3

P2Rank 0.689

Structure A0A0H3GUM8

Pocket Pocket 1

ColabFold model

FPocket 0.61 · Pocket 2

P2Rank 0.883 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 1542 / 4744 genomes with a hit

Normalized 0.325

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

6.1.1.14

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0004820 Catalysis of the reaction: ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly).
GO:0006426 The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-tRNA synthetase. The glycyll-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a glycine-accepting tRNA.
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: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.

31 records

Show feature table

Start	End	DB	Term	Name
8	288	ProSiteProfiles	PS50861	Heterodimeric glycyl-transfer RNA synthetases family profile.
8	288	InterPro	IPR006194	Glycine-tRNA synthetase, heterodimeric
6	299	PANTHER	PTHR30075	GLYCYL-TRNA SYNTHETASE
6	299	InterPro	IPR006194	Glycine-tRNA synthetase, heterodimeric
8	292	SUPERFAMILY	SSF55681	Class II aaRS and biotin synthetases
8	292	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
215	296	FunFam	G3DSA:1.20.58.180:FF:000001	Glycine--tRNA ligase alpha subunit
8	292	CDD	cd00733	GlyRS_alpha_core
8	292	InterPro	IPR002310	Glycine-tRNA ligase, alpha subunit
9	292	Pfam	PF02091	Glycyl-tRNA synthetase alpha subunit
9	292	InterPro	IPR002310	Glycine-tRNA ligase, alpha subunit
8	301	NCBIfam	TIGR00388	glycine--tRNA ligase subunit alpha
8	301	InterPro	IPR002310	Glycine-tRNA ligase, alpha subunit
215	296	Gene3D	G3DSA:1.20.58.180	Class II aaRS and biotin synthetases; domain 2
1	214	Gene3D	G3DSA:3.30.930.10	Bira Bifunctional Protein; Domain 2
1	214	InterPro	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
7	293	Hamap	MF_00254	Glycine--tRNA ligase alpha subunit [glyQ].
7	293	InterPro	IPR002310	Glycine-tRNA ligase, alpha subunit
139	159	PRINTS	PR01044	Glycyl-tRNA synthetase alpha subunit signature
139	159	InterPro	IPR002310	Glycine-tRNA ligase, alpha subunit
113	137	PRINTS	PR01044	Glycyl-tRNA synthetase alpha subunit signature
113	137	InterPro	IPR002310	Glycine-tRNA ligase, alpha subunit
253	269	PRINTS	PR01044	Glycyl-tRNA synthetase alpha subunit signature
253	269	InterPro	IPR002310	Glycine-tRNA ligase, alpha subunit
61	76	PRINTS	PR01044	Glycyl-tRNA synthetase alpha subunit signature
61	76	InterPro	IPR002310	Glycine-tRNA ligase, alpha subunit
82	102	PRINTS	PR01044	Glycyl-tRNA synthetase alpha subunit signature
82	102	InterPro	IPR002310	Glycine-tRNA ligase, alpha subunit
162	177	PRINTS	PR01044	Glycyl-tRNA synthetase alpha subunit signature
162	177	InterPro	IPR002310	Glycine-tRNA ligase, alpha subunit
1	214	FunFam	G3DSA:3.30.930.10:FF:000006	Glycine--tRNA ligase alpha subunit

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_A0A0H3GUM8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00246	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				0.376
4				0.267

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	9.01	0.483
2	8.92	0.477
3	1.64	0.027
4	1.6	0.025
5	1.27	0.013

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
2				0.61
4				0.414

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	15.04	0.743
2	1.57	0.024
3	1.32	0.014

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.

52 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
G5A	5F5W	O67081	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)…`
LMR	3RF1	A1VZ59	134.1 Da LogP -1.09 TPSA 94.8	✓ Ro5	✓ Clean	`C([C@@H](C(=O)O)O)C(=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).

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
ZINC14967098	1.000	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	1.000	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	1.000	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	1.000	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	0.737	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	0.737	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	0.737	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	0.737	346.3 Da LogP -2.75 TPSA 188.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(N)(=O)=O)[C@H](…`
ZINC1083817667	0.727	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	0.727	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	0.727	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	0.716	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	0.716	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](…`
ZINC71773889	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@H](O)C(=O)O`
ZINC71773890	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC71773891	0.667	206.1 Da LogP -1.77 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(C[C@@H](O)C(=O)O)C[C@@H](O)C(=O)O`
ZINC13547650	0.650	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	0.650	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	0.650	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	0.650	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	0.650	309.3 Da LogP -1.41 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](…`
ZINC1574270	0.636	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	0.636	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…`
ZINC24951137	0.627	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…`
ZINC5139067	0.625	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CS)[C@@H](O)[C@H]1O`
ZINC14967079	0.623	461.4 Da LogP -2.95 TPSA 258.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COS(=O)(=O)/N=C(\O)…`
ZINC5011204	0.623	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	0.623	295.3 Da LogP -1.80 TPSA 145.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COC=O)[C@@H](O)[C@…`
ZINC5011206	0.623	295.3 Da LogP -1.80 TPSA 145.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COC=O)[C@@H](O)[C@@…`
ZINC5011208	0.623	295.3 Da LogP -1.80 TPSA 145.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](COC=O)[C@@H](O)[C@…`
ZINC3814316	0.614	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]…`
ZINC4773848	0.614	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]…`
ZINC4773849	0.614	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H…`
ZINC4773850	0.614	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H…`
ZINC4773851	0.614	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@…`
ZINC77981211	0.614	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]…`
ZINC82228511	0.614	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]1O`
ZINC105372833	0.613	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@H](O…`
ZINC1532515	0.613	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@H](O…`
ZINC17107643	0.613	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC204538551	0.613	345.3 Da LogP -1.93 TPSA 197.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(N)(N)=O)[C@@H](…`
ZINC2126310	0.613	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3201893	0.613	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3830180	0.613	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](COP(=O)(O)O)[C@@H](…`
ZINC3977897	0.613	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	0.613	347.2 Da LogP -1.86 TPSA 186.1	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](COP(=O)(O)O)[C@H](O…`
ZINC4824159	0.613	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	0.613	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	0.613	344.4 Da LogP -2.42 TPSA 165.5	✓ Ro5	✓ Clean	`CS(=O)(=O)NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@…`
ZINC8613167	0.613	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.