Protein profile

KP13_00767

50S ribosomal protein L30

Genome: KpKP13

Gene: rpmD AHE42381.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GWJ3

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Amino acids 59

Annotations 4

Features 19

PDB binders 1

Druggability 0.103

Overview

Basic information about this protein and its source genome.

Accession: KP13_00767
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rpmD AHE42381.1
Status: annotated
Amino acids: 59
Structure source: AlphaFold + ColabFold

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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 100.0
DEG E-value: 5.469999999999999e-38
Localization: Cytoplasmic
ColabFold pLDDT: 94.86

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 0.103

Structure A0A0H3GWJ3

Pocket Pocket 1

P2Rank

Structure A0A0H3GWJ3

Pocket No pockets

ColabFold model

FPocket 0.076 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 503 / 4744 genomes with a hit

Normalized 0.106

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

No pockets are loaded yet for the displayed AlphaFold model AF_A0A0H3GWJ3 structure. Run experimental pocket backfill to show FPocket/P2Rank overlays on this 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_A0A0H3GWJ3	AlphaFold	—	—	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

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
NMY	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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	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.