Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: PA4671
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA4671 ctc rplY
Status: annotated
Amino acids: 204
Structure source: AlphaFold

GO

GO:0022625 The large subunit of a ribosome located in the cytosol. GO:0008097 Binding to a 5S ribosomal RNA, the smallest RNA constituent of a ribosome. GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome. GO:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
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 0.278

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5

GO:0022625 The large subunit of a ribosome located in the cytosol.
GO:0008097 Binding to a 5S ribosomal RNA, the smallest RNA constituent of a ribosome.
GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.
GO:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
2	97	Gene3D	G3DSA:2.40.240.10	Ribosomal Protein L25; Chain P
2	97	InterPro	IPR020056	Ribosomal protein L25/Gln-tRNA synthetase, N-terminal
99	196	Gene3D	G3DSA:2.170.120.20	Ribosomal protein L25, beta domain
99	196	InterPro	IPR037121	Ribosomal protein L25, C-terminal
4	188	Hamap	MF_01334	50S ribosomal protein L25 [rplY].
4	188	InterPro	IPR001021	Ribosomal protein L25, long-form
4	191	PANTHER	PTHR33284	RIBOSOMAL PROTEIN L25/GLN-TRNA SYNTHETASE, ANTI-CODON-BINDING DOMAIN-CONTAINING PROTEIN
99	196	FunFam	G3DSA:2.170.120.20:FF:000007	50S ribosomal protein L25
5	96	CDD	cd00495	Ribosomal_L25_TL5_CTC
5	96	InterPro	IPR029751	Ribosomal protein L25
6	175	NCBIfam	TIGR00731	50S ribosomal protein L25
6	175	InterPro	IPR001021	Ribosomal protein L25, long-form
2	97	FunFam	G3DSA:2.40.240.10:FF:000022	50S ribosomal protein L25
102	191	Pfam	PF14693	Ribosomal protein TL5, C-terminal domain
102	191	InterPro	IPR020057	Ribosomal protein L25, beta domain
4	196	SUPERFAMILY	SSF50715	Ribosomal protein L25-like
4	196	InterPro	IPR011035	Ribosomal protein L25/Gln-tRNA synthetase, anti-codon-binding domain superfamily
6	94	Pfam	PF01386	Ribosomal L25p family
6	94	InterPro	IPR029751	Ribosomal protein L25

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA4671	AlphaFold	—	—	full sequence	—	Viewing

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				0.278

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.

20 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
OHX	4V8E	Q5SHZ1	286.4 Da LogP -3.55 TPSA 156.1	1 viol.	✓ Clean	`N[Os](N)(N)(N)(N)N`
SPD	4WFA	Q2FJE0	145.2 Da LogP -0.34 TPSA 64.1	✓ Ro5	✓ Clean	`C(CCNCCCN)CN`

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
ZINC27564039	0.933	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCNCCCN`
ZINC13377742	0.929	230.4 Da LogP 0.42 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCCNCCCCN`
ZINC1532734	0.929	202.3 Da LogP -0.36 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCNCCCCNCCCN`
ZINC1598087	0.867	215.4 Da LogP 1.61 TPSA 64.1	✓ Ro5	✓ Clean	`NCCCCCCNCCCCCCN`
ZINC100056474	0.650	270.5 Da LogP 4.63 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCNCCCN`
ZINC107767463	0.650	200.4 Da LogP 2.68 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCNCCCCCCN`
ZINC59496006	0.650	242.5 Da LogP 3.85 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNCCCN`
ZINC22465713	0.563	232.4 Da LogP -2.74 TPSA 100.2	1 viol.	✓ Clean	`NCCNCCNCCNCCNCCN`
ZINC31361891	0.550	200.3 Da LogP -0.58 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCNC/C=C/CNCCCN`
ZINC4978005	0.550	200.3 Da LogP -0.58 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCNC/C=C\CNCCCN`
ZINC169723055	0.542	228.3 Da LogP 1.00 TPSA 98.8	✓ Ro5	Alert	`[N-]=[N+]=NCCCNCCCCNCCCN`
ZINC100638283	0.524	200.4 Da LogP 2.68 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCCCCCNCCN`
ZINC100967545	0.524	256.5 Da LogP 4.24 TPSA 38.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCNCCN`
ZINC1857785994	0.520	271.5 Da LogP -0.33 TPSA 70.5	✓ Ro5	✓ Clean	`NCCCCNCCN1CCN(CCCCN)CC1`
ZINC3870097	0.520	244.4 Da LogP -0.18 TPSA 79.2	✓ Ro5	✓ Clean	`CC(=O)NCCCNCCCCNCCCN`
ZINC1857786606	0.500	327.6 Da LogP 1.23 TPSA 70.5	✓ Ro5	✓ Clean	`NCCCCCCNCCN1CCN(CCCCCCN)CC1`
ZINC2265381413	0.500	439.8 Da LogP 4.35 TPSA 70.5	✓ Ro5	✓ Clean	`NCCCCCCCCCCNCCN1CCN(CCCCCCCCCCN)CC1`
ZINC60047046	0.500	271.5 Da LogP 3.05 TPSA 50.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCNCCNCCN`

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.

PA4671