Protein profile

PA4672

peptidyl-tRNA hydrolase

Genome: NC_002516.2

Gene: PA4672 pth Structure source: Experimental + AlphaFold UniProt Q9HVC3

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Amino acids 194

Annotations 6

Features 19

PDB binders 10

Druggability 0.619

Overview

Basic information about this protein and its source genome.

Accession: PA4672
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4672 pth
Status: annotated
Amino acids: 194
Structure source: Experimental + AlphaFold

3.1.1.29

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0004045 Catalysis of the reaction: an N-acyl-L-alpha-aminoacyl-tRNA + H2O = an N-acyl-L-amino acid + a tRNA + H+. GO:0000049 Binding to a transfer RNA. GO:0006515 The chemical reactions and pathways resulting in the breakdown of misfolded or attenuated proteins. GO:0072344 A process of cytosolic translational elongation that takes place when a cytosolic ribosome has stalled during translation, and results in freeing the ribosome from the stalled translation complex.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 40.12
Human E-value: 1.02e-25
Gut microbiome off-target: hit
Essential (DEG): Y
Localization: Cytoplasmic

Selected Druggability evidence

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 0.619

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

3.1.1.29

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0004045 Catalysis of the reaction: an N-acyl-L-alpha-aminoacyl-tRNA + H2O = an N-acyl-L-amino acid + a tRNA + H+.
GO:0000049 Binding to a transfer RNA.
GO:0006515 The chemical reactions and pathways resulting in the breakdown of misfolded or attenuated proteins.
GO:0072344 A process of cytosolic translational elongation that takes place when a cytosolic ribosome has stalled during translation, and results in freeing the ribosome from the stalled translation complex.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
6	178	CDD	cd00462	PTH
6	178	InterPro	IPR001328	Peptidyl-tRNA hydrolase
1	194	Gene3D	G3DSA:3.40.50.1470	-
1	194	InterPro	IPR036416	Peptidyl-tRNA hydrolase superfamily
5	188	PANTHER	PTHR17224	PEPTIDYL-TRNA HYDROLASE
5	188	InterPro	IPR001328	Peptidyl-tRNA hydrolase
17	30	ProSitePatterns	PS01195	Peptidyl-tRNA hydrolase signature 1.
17	30	InterPro	IPR018171	Peptidyl-tRNA hydrolase, conserved site
6	190	Pfam	PF01195	Peptidyl-tRNA hydrolase
6	190	InterPro	IPR001328	Peptidyl-tRNA hydrolase
111	121	ProSitePatterns	PS01196	Peptidyl-tRNA hydrolase signature 2.
111	121	InterPro	IPR018171	Peptidyl-tRNA hydrolase, conserved site
1	193	FunFam	G3DSA:3.40.50.1470:FF:000001	Peptidyl-tRNA hydrolase
4	183	Hamap	MF_00083	Peptidyl-tRNA hydrolase [pth].
4	183	InterPro	IPR001328	Peptidyl-tRNA hydrolase
5	172	NCBIfam	TIGR00447	aminoacyl-tRNA hydrolase
5	172	InterPro	IPR001328	Peptidyl-tRNA hydrolase
5	191	SUPERFAMILY	SSF53178	Peptidyl-tRNA hydrolase-like
5	191	InterPro	IPR036416	Peptidyl-tRNA hydrolase superfamily

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

9 + 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 4QAJ	X-ray	1.50 Å	A	100.0% 1-194	PDBe RCSB PDBj File	Viewing
PDB 4QBK	X-ray	1.77 Å	A	100.0% 1-194	PDBe RCSB PDBj File	Loaded
PDB 4QD3	X-ray	1.89 Å	A	100.0% 1-194	PDBe RCSB PDBj File	Loaded
PDB 4FNO	X-ray	2.25 Å	A,B	100.0% 1-194	PDBe RCSB PDBj File	Loaded
PDB 4JC4	X-ray	2.25 Å	A	100.0% 1-194	PDBe RCSB PDBj File	Loaded
PDB 4DHW	X-ray	2.43 Å	A,B	100.0% 1-194	PDBe RCSB PDBj File	Loaded
PDB 4ERX	X-ray	2.50 Å	A,B	100.0% 1-194	PDBe RCSB PDBj File	Loaded
PDB 4DJJ	X-ray	2.94 Å	A,B	100.0% 1-194	PDBe RCSB PDBj File	Loaded
PDB 4FYJ	X-ray	1.77 Å	A	99.0% 2-193	PDBe RCSB PDBj File	Loaded
AlphaFold PA4672	AlphaFold	—	—	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				0.619

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				5.61	0.27
2				5.16	0.238

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				0.596

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.

60 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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
0L1	4DHW 2.43 Å Open crystal	146.1 Da LogP 0.72 TPSA 74.6	✓ Ro5	✓ Clean	`C(CCC(=O)O)CC(=O)O`
3NZ	4QBK 1.77 Å Open crystal	443.5 Da LogP -1.28 TPSA 183.7	1 viol.	✓ Clean	`COc1ccc(cc1)C[C@@H](C(=O)N[C@@H]2[C@H](O[C@H]([…`
5AE	4QD3 1.89 Å Open crystal	244.2 Da LogP -3.17 TPSA 143.7	✓ Ro5	✓ Clean	`C1=NC(=NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)CO)…`
PML	4DJJ 2.94 Å Open crystal	160.2 Da LogP 1.11 TPSA 74.6	✓ Ro5	✓ Clean	`C(CCC(=O)O)CCC(=O)O`

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
AR3	5Y9A	D0C9L6	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`C1=CN(C(=O)N=C1N)[C@H]2[C@H]([C@@H]([C@H](O2)CO…`
CTN	4JWK	D0C9L6	243.2 Da LogP -2.56 TPSA 130.8	✓ Ro5	✓ Clean	`C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`
FLC	5ZX8	Q5SHZ2	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
POL	6IX6	D0C9L6	60.1 Da LogP 0.39 TPSA 20.2	✓ Ro5	✓ Clean	`CCCO`
TLA	4OLJ	D0C9L6	150.1 Da LogP -2.12 TPSA 115.1	✓ Ro5	✓ Clean	`[C@@H]([C@H](C(=O)O)O)(C(=O)O)O`
URI	4JX9	D0C9L6	244.2 Da LogP -2.85 TPSA 124.8	✓ Ro5	✓ Clean	`C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)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
ZINC1078622	1.000	244.2 Da LogP -3.17 TPSA 143.7	✓ Ro5	✓ Clean	`Nc1ncn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c(=O)…`
ZINC11592974	1.000	244.2 Da LogP -3.17 TPSA 143.7	✓ Ro5	✓ Clean	`Nc1ncn([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c(=O…`
ZINC11592975	1.000	244.2 Da LogP -3.17 TPSA 143.7	✓ Ro5	✓ Clean	`Nc1ncn([C@@H]2O[C@H](CO)[C@@H](O)[C@@H]2O)c(=O)…`
ZINC13547768	1.000	244.2 Da LogP -3.17 TPSA 143.7	✓ Ro5	✓ Clean	`Nc1ncn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2O)c(=O)n1`
ZINC21984062	1.000	244.2 Da LogP -3.17 TPSA 143.7	✓ Ro5	✓ Clean	`Nc1ncn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2O)c(=O)n1`
ZINC3830251	1.000	244.2 Da LogP -3.17 TPSA 143.7	✓ Ro5	✓ Clean	`Nc1ncn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2O)c(=O)n1`
ZINC3830252	1.000	244.2 Da LogP -3.17 TPSA 143.7	✓ Ro5	✓ Clean	`Nc1ncn([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2O)c(=O)…`
ZINC3861768	1.000	244.2 Da LogP -3.17 TPSA 143.7	✓ Ro5	✓ Clean	`Nc1ncn([C@@H]2O[C@H](CO)[C@@H](O)[C@H]2O)c(=O)n1`
ZINC4830897	1.000	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	1.000	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	1.000	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	1.000	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…`
ZINC967756	1.000	244.2 Da LogP -3.17 TPSA 143.7	✓ Ro5	✓ Clean	`Nc1ncn([C@H]2O[C@@H](CO)[C@H](O)[C@@H]2O)c(=O)n1`
ZINC1529497	0.917	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045	0.917	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115	0.917	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020	0.917	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440	0.917	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298	0.917	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062	0.917	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC53147178	0.829	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	0.829	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	0.829	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	0.829	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	0.829	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	0.829	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	0.829	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	0.829	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	0.829	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	0.829	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	0.829	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	0.829	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	0.829	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…`
ZINC4824413	0.806	413.4 Da LogP -1.29 TPSA 174.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](NC(=O)[C@…`
ZINC4824417	0.806	413.4 Da LogP -1.29 TPSA 174.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](NC(=O)[C@…`
ZINC4824420	0.806	413.4 Da LogP -1.29 TPSA 174.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](NC(=O)[C@@…`
ZINC4824422	0.806	413.4 Da LogP -1.29 TPSA 174.4	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](NC(=O)[C@H…`
ZINC13546398	0.800	246.2 Da LogP -1.87 TPSA 104.5	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@H]2F)c(=O)[…`
ZINC195751891	0.800	246.2 Da LogP -1.87 TPSA 104.5	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO)[C@H](O)[C@H]2F)c(=O)…`
ZINC21999985	0.800	246.2 Da LogP -1.87 TPSA 104.5	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO)[C@H](O)[C@@H]2F)c(=O)…`
ZINC2570870	0.800	246.2 Da LogP -1.87 TPSA 104.5	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO)[C@H](O)[C@H]2F)c(=O)[…`
ZINC26657838	0.800	243.2 Da LogP -2.89 TPSA 130.6	✓ Ro5	✓ Clean	`N[C@@H]1[C@H](O)[C@@H](CO)O[C@@H]1n1ccc(=O)[nH]…`
ZINC26657844	0.800	243.2 Da LogP -2.89 TPSA 130.6	✓ Ro5	✓ Clean	`N[C@H]1[C@H](O)[C@@H](CO)O[C@@H]1n1ccc(=O)[nH]c…`
ZINC34248194	0.800	243.2 Da LogP -2.89 TPSA 130.6	✓ Ro5	✓ Clean	`N[C@@H]1[C@H](O)[C@H](CO)O[C@@H]1n1ccc(=O)[nH]c…`
ZINC34248196	0.800	243.2 Da LogP -2.89 TPSA 130.6	✓ Ro5	✓ Clean	`N[C@@H]1[C@H](O)[C@H](CO)O[C@H]1n1ccc(=O)[nH]c1…`
ZINC34248200	0.800	243.2 Da LogP -2.89 TPSA 130.6	✓ Ro5	✓ Clean	`N[C@H]1[C@H](O)[C@H](CO)O[C@H]1n1ccc(=O)[nH]c1=O`
ZINC5541271	0.800	246.2 Da LogP -1.87 TPSA 104.5	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@H]2F)c(=O)…`
ZINC5541274	0.800	246.2 Da LogP -1.87 TPSA 104.5	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@H]2F)c(=O…`
ZINC5541275	0.800	246.2 Da LogP -1.87 TPSA 104.5	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO)[C@@H](O)[C@@H]2F)c(=O…`
ZINC5541279	0.800	246.2 Da LogP -1.87 TPSA 104.5	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO)[C@@H](O)[C@@H]2F)c(=…`

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.