KpKP13 Protein target profile

D-tyrosyl-tRNA(Tyr) deacylase

Accession: KP13_00617

Gene: AHE47091.1 dtd 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GG72

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Length 145

Pocket druggability (P2Rank · AlphaFold DB model) 0.157

Direct ligand evidence 0 54 total records

Functional annotation 2 EC 8 GO

Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.78. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 4 structural and 0 bioactivity records.

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target: Hit
Human identity (%): 37.415 Lower values reduce human off-target concern.
Human E-value: 3.6499999999999996e-24
Gut microbiome similarity: 15.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 40.972 Higher values support similarity to known essential genes.
DEG E-value: 1.29e-36 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 98.13 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.157

Structure A0A0H3GG72

Pocket Pocket 1

Druggability (FPocket) 0.778

Structure A0A0H3GG72

Pocket Pocket 1

ColabFold model

P2Rank 0.137 · Pocket 1

FPocket 0.673 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 725 / 4744 genomes with a hit

Prevalence 15.3%

Sequence

Primary amino-acid sequence viewer.

MIALIQRVSRASVTVADEVTGEIGPGLLVLLGVEKDDDEQKANRLCERVLGYRIFSDAEGKMNLNVQQAGGSVLVVSQFTLAADTERGMRPSFSKGAAPDRAEALYEYFVARCRQQEMHTQTGRFAADMQVSLVNDGPVTFWLQV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 8 GO

Subcellular localization

Localization: Unknown

Enzyme Commission (EC)

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0051499 Catalysis of the reaction: a D-aminoacyl-tRNA + H2O = a D-alpha-amino acid + a tRNA + H+. Removal of a D-amino acid from a charged tRNA.
GO:0002161 The hydrolysis of an incorrectly aminoacylated tRNA.
GO:0051500 Catalysis of the reaction: D-tyrosyl-tRNATyr + H2O = D-tyrosine + tRNATyr. Removal of a D-tyrosine from a charged tRNA(Tyr).
GO:0106026 Catalysis of the reaction: glycyl-tRNA(Ala) + H2O = tRNA(Ala) + glycine + H+.
GO:0043908 Catalysis of the hydrolysis of misacylated Ser-tRNA(Ala) and Gly-tRNA(Ala).
GO:0000049 Binding to a transfer RNA.
GO:0019478 The chemical reactions and pathways resulting in the breakdown of D-amino acids, the D-enantiomers of amino acids.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
1	144	PANTHER	PTHR10472	D-TYROSYL-TRNA TYR DEACYLASE
1	144	InterPro	IPR003732	D-aminoacyl-tRNA deacylase DTD
1	145	Hamap	MF_00518	D-aminoacyl-tRNA deacylase [dtd].
1	145	InterPro	IPR003732	D-aminoacyl-tRNA deacylase DTD
1	145	CDD	cd00563	Dtyr_deacylase
1	145	FunFam	G3DSA:3.50.80.10:FF:000001	D-aminoacyl-tRNA deacylase
3	144	Pfam	PF02580	D-Tyr-tRNA(Tyr) deacylase
3	144	InterPro	IPR003732	D-aminoacyl-tRNA deacylase DTD
1	145	Gene3D	G3DSA:3.50.80.10	-
1	145	InterPro	IPR023509	D-aminoacyl-tRNA deacylase-like superfamily
1	145	NCBIfam	TIGR00256	D-aminoacyl-tRNA deacylase
1	144	SUPERFAMILY	SSF69500	DTD-like
1	144	InterPro	IPR023509	D-aminoacyl-tRNA deacylase-like superfamily

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low

How colors and pocket overlays are used

Uniform protein color marks the displayed model as a single molecular object.

Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.

Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.

'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.

'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.

'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.157

Likely same site as FPocket 1 2.6 Å 11 shared residues 100% of smaller site

Show in viewer

Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1

0.778

Likely same site as P2Rank 1 2.6 Å 11 shared residues 100% of smaller site

Show in viewer

Surrounding area

All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold DB AF_A0A0H3GG72	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_00617	ColabFold	—	—	full sequence	—	Loaded

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.

54 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 4 records from similar proteins

Structural ligands 4 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

A3G PDB via homolog 323.3 Da · LogP -2.90 · TPSA 174.4 Open detail RCSB PDB

D3Y PDB via homolog Detail RCSB PDB

DAR PDB via homolog Detail RCSB PDB

DHI PDB via homolog Detail RCSB PDB

ZINC4824413 ZINC proposed compound · Tanimoto 0.857 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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
A3G RCSB PDB	5J61	Q8IIS0	323.3 Da LogP -2.90 TPSA 174.4	✓ Ro5	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
D3Y RCSB PDB	4NBI	Q8IIS0	429.4 Da LogP -1.58 TPSA 194.7	2 viol.	✓ Clean	`c1cc(ccc1C[C@H](C(=O)N[C@@H]2[C@H](O[C@H]([C@@H…`
DAR RCSB PDB	3KO9	Q8IIS0	175.2 Da LogP -3.16 TPSA 127.0	✓ Ro5	✓ Clean	`C(C[C@H](C(=O)O)N)CNC(=[NH2+])N`
DHI RCSB PDB	3KOC	Q8IIS0	156.2 Da LogP -1.22 TPSA 93.2	✓ Ro5	✓ Clean	`c1c([nH+]c[nH]1)C[C@H](C(=O)O)N`

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
ZINC4824413 ZINC	0.857	413.4 Da LogP -1.29 TPSA 174.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](NC(=O)[C@…`
ZINC4824417 ZINC	0.857	413.4 Da LogP -1.29 TPSA 174.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](NC(=O)[C@…`
ZINC4824420 ZINC	0.857	413.4 Da LogP -1.29 TPSA 174.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](NC(=O)[C@@…`
ZINC4824422 ZINC	0.857	413.4 Da LogP -1.29 TPSA 174.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](NC(=O)[C@H…`
ZINC4830897 ZINC	0.821	443.5 Da LogP -1.28 TPSA 183.7	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@H](n…`
ZINC4830899 ZINC	0.821	443.5 Da LogP -1.28 TPSA 183.7	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@H](…`
ZINC4830900 ZINC	0.821	443.5 Da LogP -1.28 TPSA 183.7	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@H]2[C@H](CO)O[C@H](n3…`
ZINC4830901 ZINC	0.821	443.5 Da LogP -1.28 TPSA 183.7	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@H]2[C@H](CO)O[C@H](n…`
ZINC4830892 ZINC	0.750	280.3 Da LogP -1.75 TPSA 131.3	✓ Ro5	✓ Clean	`CN[C@@H]1[C@H](CO)O[C@H](n2cnc3c(N)ncnc32)[C@@H…`
ZINC4830894 ZINC	0.750	280.3 Da LogP -1.75 TPSA 131.3	✓ Ro5	✓ Clean	`CN[C@H]1[C@H](CO)O[C@H](n2cnc3c(N)ncnc32)[C@@H]…`
ZINC4830895 ZINC	0.750	280.3 Da LogP -1.75 TPSA 131.3	✓ Ro5	✓ Clean	`CN[C@@H]1[C@@H](CO)O[C@H](n2cnc3c(N)ncnc32)[C@@…`
ZINC4830896 ZINC	0.750	280.3 Da LogP -1.75 TPSA 131.3	✓ Ro5	✓ Clean	`CN[C@H]1[C@@H](CO)O[C@H](n2cnc3c(N)ncnc32)[C@@H…`
ZINC4825167 ZINC	0.746	484.5 Da LogP -1.78 TPSA 203.5	2 viol.	✓ Clean	`C[C@H](NC(=O)[C@H](N)Cc1ccccc1)C(=O)N[C@@H]1[C@…`
ZINC4825172 ZINC	0.746	484.5 Da LogP -1.78 TPSA 203.5	2 viol.	✓ Clean	`C[C@@H](NC(=O)[C@H](N)Cc1ccccc1)C(=O)N[C@@H]1[C…`
ZINC4825178 ZINC	0.746	484.5 Da LogP -1.78 TPSA 203.5	2 viol.	✓ Clean	`C[C@H](NC(=O)[C@H](N)Cc1ccccc1)C(=O)N[C@H]1[C@H…`
ZINC4825185 ZINC	0.746	484.5 Da LogP -1.78 TPSA 203.5	2 viol.	✓ Clean	`C[C@@H](NC(=O)[C@H](N)Cc1ccccc1)C(=O)N[C@H]1[C@…`
ZINC4830518 ZINC	0.716	395.4 Da LogP -2.66 TPSA 211.7	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](NC(=O)[C@…`
ZINC4830519 ZINC	0.716	395.4 Da LogP -2.66 TPSA 211.7	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](NC(=O)[C…`
ZINC4830520 ZINC	0.716	395.4 Da LogP -2.66 TPSA 211.7	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](NC(=O)[C@…`
ZINC4830521 ZINC	0.716	395.4 Da LogP -2.66 TPSA 211.7	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](NC(=O)[C…`
ZINC4824650 ZINC	0.710	394.4 Da LogP -2.40 TPSA 200.5	2 viol.	✓ Clean	`NCCCC[C@@H](N)C(=O)N[C@@H]1[C@H](CO)O[C@H](n2cn…`
ZINC4824652 ZINC	0.710	394.4 Da LogP -2.40 TPSA 200.5	2 viol.	✓ Clean	`NCCCC[C@@H](N)C(=O)N[C@@H]1[C@H](CO)O[C@@H](n2c…`
ZINC4824654 ZINC	0.710	394.4 Da LogP -2.40 TPSA 200.4	2 viol.	✓ Clean	`NCCCC[C@@H](N)C(=O)N[C@H]1[C@H](O)[C@@H](n2cnc3…`
ZINC4824655 ZINC	0.710	394.4 Da LogP -2.40 TPSA 200.4	2 viol.	✓ Clean	`NCCCC[C@@H](N)C(=O)N[C@H]1[C@H](O)[C@H](n2cnc3c…`
ZINC4809089 ZINC	0.692	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](S)[C@H]1O`
ZINC4809090 ZINC	0.692	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](S)[C@H]1O`
ZINC4809091 ZINC	0.692	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](S)[C@@H]1O`
ZINC4809092 ZINC	0.692	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](S)[C@@H]…`
ZINC53147178 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@@H…`
ZINC53147179 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@@H]…`
ZINC58994963 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@@H]…`
ZINC59065899 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](O)[C@@H](n…`
ZINC59817042 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@H](…`
ZINC59817043 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@H]2[C@H](O)[C@@H](n3…`
ZINC59817045 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@H]2[C@H](O)[C@H](n3c…`
ZINC61389312 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@H](…`
ZINC71789712 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@@H](N)C(=O)N[C@@H]2[C@@H](CO)O[C@H]…`
ZINC73333306 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@H](n…`
ZINC73333309 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@@H]2[C@H](CO)O[C@@H](…`
ZINC73333313 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@H]2[C@H](O)[C@@H](n3c…`
ZINC73333316 ZINC	0.676	471.5 Da LogP -0.79 TPSA 160.9	1 viol.	✓ Clean	`COc1ccc(C[C@H](N)C(=O)N[C@H]2[C@H](O)[C@H](n3cn…`
ZINC2047403 ZINC	0.673	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1O`
ZINC2169830 ZINC	0.673	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC3201878 ZINC	0.673	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC3830178 ZINC	0.673	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3978047 ZINC	0.673	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC3978049 ZINC	0.673	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC8580514 ZINC	0.673	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC895113 ZINC	0.673	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC970363 ZINC	0.673	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`

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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GG72