Protein profile

VK055_3290

D-tyrosyl-tRNA(Tyr) deacylase

Genome: KpATCC43816

Gene: AIK81851.1 dtd Structure source: AlphaFold + ColabFold UniProt A0A0H3GG72

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Amino acids 131

Annotations 10

Features 13

PDB binders 4

Druggability 0.778

Overview

Basic information about this protein and its source genome.

Accession: VK055_3290
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK81851.1 dtd
Status: annotated
Amino acids: 131
Structure source: AlphaFold + ColabFold

3.1.1.96 3.1.1.-

GO:0002161 The hydrolysis of an incorrectly aminoacylated tRNA. 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: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).

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 34.4
Human E-value: 1.31e-16
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 39.844
Localization: Unknown
ColabFold pLDDT: 96.36

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 0.778

Structure A0A0H3GG72

Pocket Pocket 1

P2Rank 0.157

Structure A0A0H3GG72

Pocket Pocket 1

ColabFold model

FPocket 0.074 · Pocket 8

P2Rank 0.257 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 678 / 4744 genomes with a hit

Normalized 0.143

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 8 GO

Enzyme Commission (EC)

Gene Ontology (GO)

GO:0002161 The hydrolysis of an incorrectly aminoacylated tRNA.
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: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 Features

Domain/signature hits from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
1	131	Gene3D	G3DSA:3.50.80.10	-
1	131	InterPro	IPR023509	D-aminoacyl-tRNA deacylase-like superfamily
3	131	CDD	cd00563	Dtyr_deacylase
3	131	InterPro	IPR003732	D-aminoacyl-tRNA deacylase DTD
3	130	PANTHER	PTHR10472	D-TYROSYL-TRNA TYR DEACYLASE
3	130	InterPro	IPR003732	D-aminoacyl-tRNA deacylase DTD
3	130	SUPERFAMILY	SSF69500	DTD-like
3	130	InterPro	IPR023509	D-aminoacyl-tRNA deacylase-like superfamily
1	131	Hamap	MF_00518	D-aminoacyl-tRNA deacylase [dtd].
1	131	InterPro	IPR003732	D-aminoacyl-tRNA deacylase DTD
3	131	NCBIfam	TIGR00256	D-aminoacyl-tRNA deacylase
3	130	Pfam	PF02580	D-Tyr-tRNA(Tyr) deacylase
1	131	FunFam	G3DSA:3.50.80.10:FF:000001	D-aminoacyl-tRNA deacylase

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_A0A0H3GG72	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_3290	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				0.778

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				4.05	0.162

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	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				5.96	0.293
2				3.99	0.159

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

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
A3G	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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.