KpKP13 Protein target profile

50S ribosomal protein L30

Accession: KP13_00767

Gene: rpmD AHE42381.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GWJ3

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Length 59

Pocket druggability (FPocket · AlphaFold DB model) 0.103

Direct ligand evidence 0 51 total records

Functional annotation 0 EC 4 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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

Main supporting evidence

Risks to review

Microbiome similarity 503 of 4744 screened genomes (10.6%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.10.

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: No hit
Gut microbiome similarity: 10.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 100.0 Higher values support similarity to known essential genes.
DEG E-value: 5.469999999999999e-38 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 94.86 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)

Structure A0A0H3GWJ3

Pocket No pockets

Druggability (FPocket) 0.103

Structure A0A0H3GWJ3

Pocket Pocket 1

ColabFold model

FPocket 0.076 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 503 / 4744 genomes with a hit

Prevalence 10.6%

Sequence

Primary amino-acid sequence viewer.

MAKTIKITQTRSAIGRLPKHKATLLGLGLRRIGHTVEREDTPAVRGMVNAVSFMVKVEE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.
GO:0015934 The larger of the two subunits of a ribosome. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site).
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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
5	59	NCBIfam	TIGR01308	50S ribosomal protein L30
5	59	InterPro	IPR005996	Ribosomal protein L30, bacterial-type
3	59	SUPERFAMILY	SSF55129	Ribosomal protein L30p/L7e
3	59	InterPro	IPR036919	Ribosomal protein L30, ferredoxin-like fold domain superfamily
5	55	Pfam	PF00327	Ribosomal protein L30p/L7e
5	55	InterPro	IPR016082	Ribosomal protein L30, ferredoxin-like fold domain
2	59	Hamap	MF_01371_B	50S ribosomal protein L30 [rpmD].
2	59	InterPro	IPR005996	Ribosomal protein L30, bacterial-type
3	59	PANTHER	PTHR15892	MITOCHONDRIAL RIBOSOMAL PROTEIN L30
3	59	InterPro	IPR005996	Ribosomal protein L30, bacterial-type
1	59	PIRSF	PIRSF002211	RPL30p
1	59	InterPro	IPR005996	Ribosomal protein L30, bacterial-type
5	58	CDD	cd01658	Ribosomal_L30
5	58	InterPro	IPR005996	Ribosomal protein L30, bacterial-type
1	59	FunFam	G3DSA:3.30.1390.20:FF:000001	50S ribosomal protein L30
1	59	Gene3D	G3DSA:3.30.1390.20	-
1	59	InterPro	IPR036919	Ribosomal protein L30, ferredoxin-like fold domain superfamily
23	55	ProSitePatterns	PS00634	Ribosomal protein L30 signature.
23	55	InterPro	IPR018038	Ribosomal protein L30, conserved site

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.

Download VMD script Full viewer

No pockets are loaded yet for the displayed AlphaFold DB model AF_A0A0H3GWJ3 structure. Run experimental pocket backfill to show FPocket/P2Rank overlays on this structure.

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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'.

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_A0A0H3GWJ3	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_00767	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.

51 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

NMY PDB via homolog 614.7 Da · LogP -8.90 · TPSA 353.1 Open detail RCSB PDB

ZINC100052153 ZINC proposed compound · Tanimoto 0.881 Detail ZINC

ZINC100223147 ZINC proposed compound · Tanimoto 0.881 Detail ZINC

ZINC103649633 ZINC proposed compound · Tanimoto 0.881 Detail ZINC

ZINC242575106 ZINC proposed compound · Tanimoto 0.881 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
NMY RCSB PDB	4V9C	P0AG51	614.7 Da LogP -8.90 TPSA 353.1	3 viol.	✓ Clean	`C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[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
ZINC100052153 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC100223147 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@@H](O[C@@H]3O[C@H](…`
ZINC103649633 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242575106 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@@H]3O[C@H](CO…`
ZINC242575107 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@@H]3O[C@H](CO…`
ZINC242575108 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@@H]3O[C@H](CO…`
ZINC242575109 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@@H]3O[C@H](CO…`
ZINC43664294 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@H]3O[C@@H](CO…`
ZINC43664297 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@H]3O[C@@H](CO…`
ZINC43664300 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@H]3O[C@@H](CO…`
ZINC43664303 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O[C@H]3O[C@@H](CO…`
ZINC53255716 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC56874669 ZINC	0.881	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC60184027 ZINC	0.786	455.5 Da LogP -6.62 TPSA 256.6	2 viol.	✓ Clean	`N[C@H]1C[C@@H](N)[C@H](O)[C@@H](O[C@@H]2O[C@H](…`
ZINC256001609 ZINC	0.717	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC256001610 ZINC	0.717	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC256001611 ZINC	0.717	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC256001612 ZINC	0.717	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC53132258 ZINC	0.717	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC77301567 ZINC	0.717	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@H]2[C@H](N)C[C@H](N)[C@@H](O…`
ZINC245224241 ZINC	0.698	322.4 Da LogP -5.12 TPSA 203.5	1 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O)[C@@H]…`
ZINC245224242 ZINC	0.698	322.4 Da LogP -5.12 TPSA 203.5	1 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O)[C@@H]…`
ZINC245224243 ZINC	0.698	322.4 Da LogP -5.12 TPSA 203.5	1 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O)[C@@H]…`
ZINC255189913 ZINC	0.698	322.4 Da LogP -5.12 TPSA 203.5	1 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC4095654 ZINC	0.698	322.4 Da LogP -5.12 TPSA 203.5	1 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC45076909 ZINC	0.698	322.4 Da LogP -5.12 TPSA 203.5	1 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC45076911 ZINC	0.698	322.4 Da LogP -5.12 TPSA 203.5	1 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@@H](N)[C@H]…`
ZINC59846619 ZINC	0.698	322.4 Da LogP -5.12 TPSA 203.5	1 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O)[C@@H]…`
ZINC59846620 ZINC	0.698	322.4 Da LogP -5.12 TPSA 203.5	1 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O)[C@H](…`
ZINC17654095 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@…`
ZINC1857793042 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC239203289 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC239203290 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC239203291 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC239203292 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC242649355 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649358 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649360 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649362 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC245224172 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224173 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224174 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224175 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC43470138 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H…`
ZINC8101132 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@H]3O…`
ZINC8101133 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@H]3O…`
ZINC8101134 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@H](O[C@H]3O[…`
ZINC8101135 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@H](O[C@H]3O[…`
ZINC8214590 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC8217403 ZINC	0.625	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`

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 A0A0H3GWJ3