Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: KP13_00765
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rplR AHE42379.1
Status: annotated
Amino acids: 117
Structure source: AlphaFold + ColabFold

GO

GO:0003735 The action of a molecule that contributes to the structural integrity of 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. 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: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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 39.189
Human E-value: 1.2e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 100.0
DEG E-value: 3.0299999999999997e-81
Localization: Cytoplasmic
ColabFold pLDDT: 93.18

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 0.323

Structure A0A0H3GU14

Pocket Pocket 3

P2Rank

Structure A0A0H3GU14

Pocket No pockets

ColabFold model

FPocket 0.154 · Pocket 3

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 1566 / 4744 genomes with a hit

Normalized 0.33

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:0003735 The action of a molecule that contributes to the structural integrity of 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.
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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
17	115	CDD	cd00432	Ribosomal_L18_L5e
2	117	Hamap	MF_01337_B	50S ribosomal protein L18 [rplR].
2	117	InterPro	IPR004389	Ribosomal protein L18, bacterial-type
9	117	PANTHER	PTHR12899	39S RIBOSOMAL PROTEIN L18, MITOCHONDRIAL
9	117	InterPro	IPR005484	Ribosomal protein L18
3	117	NCBIfam	TIGR00060	50S ribosomal protein L18
3	117	InterPro	IPR004389	Ribosomal protein L18, bacterial-type
3	115	SUPERFAMILY	SSF53137	Translational machinery components
1	117	Gene3D	G3DSA:3.30.420.100	-
1	117	Pfam	PF00861	Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast
1	117	InterPro	IPR005484	Ribosomal protein L18
1	21	Coils	Coil	Coil
1	117	FunFam	G3DSA:3.30.420.100:FF:000001	50S ribosomal protein L18

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_A0A0H3GU14	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00765	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				0.323

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.

12 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
PUT	6I7V	P0C018	88.2 Da LogP -0.32 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CN`
T1C	6YSI	D0CD13	587.7 Da LogP -2.19 TPSA 208.2	2 viol.	✓ Clean	`CC(C)(C)NCC(=O)Nc1cc(c2c(c1O)C(=O)C3=C([C@]4([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
ZINC1685531	0.875	200.4 Da LogP 2.80 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCN`
ZINC34273707	0.875	256.5 Da LogP 4.37 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCCCN`
ZINC5178646	0.875	228.4 Da LogP 3.59 TPSA 52.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCN`
ZINC13377742	0.538	230.4 Da LogP 0.42 TPSA 76.1	✓ Ro5	✓ Clean	`NCCCCNCCCCNCCCCN`
ZINC1545440	0.538	213.4 Da LogP 4.65 TPSA 26.0	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCN`
ZINC2385445	0.538	201.4 Da LogP 2.84 TPSA 46.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCO`
ZINC34196183	0.538	229.4 Da LogP 3.62 TPSA 46.2	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCO`
ZINC38585283	0.538	203.4 Da LogP 3.39 TPSA 26.0	✓ Ro5	✓ Clean	`NCCCCCCCCCCCS`
ZINC38684714	0.538	230.4 Da LogP 0.51 TPSA 81.3	✓ Ro5	✓ Clean	`NCCCCN(CCCCN)CCCCN`
ZINC1598087	0.500	215.4 Da LogP 1.61 TPSA 64.1	✓ Ro5	✓ Clean	`NCCCCCCNCCCCCCN`

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.

KP13_00765