Protein profile

KP13_01811

30S ribosomal protein S2

Genome: KpKP13

Gene: AHE46251.1 rpsB Structure source: AlphaFold + ColabFold UniProt A0A0H3GS30

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Amino acids 241

Annotations 5

Features 31

PDB binders 2

Druggability 0.332

Overview

Basic information about this protein and its source genome.

Accession: KP13_01811
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46251.1 rpsB
Status: annotated
Amino acids: 241
Structure source: AlphaFold + ColabFold

GO:0015935 The smaller of the two subunits of a 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. GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome. GO:0022627 The small subunit of a ribosome located in the cytosol.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 30.622
Human E-value: 4.0000000000000004e-23
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 98.755
DEG E-value: 1.8499999999999999e-180
Localization: Cytoplasmic
ColabFold pLDDT: 94.47

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 0.332

Structure A0A0H3GS30

Pocket Pocket 15

P2Rank

Structure A0A0H3GS30

Pocket No pockets

ColabFold model

FPocket 0.7 · Pocket 1

P2Rank 0.069 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 3340 / 4744 genomes with a hit

Normalized 0.704

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

GO:0015935 The smaller of the two subunits of a 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.
GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.
GO:0022627 The small subunit of a ribosome located in the cytosol.

Sequence Features

Domain/signature hits from InterPro and related databases.

31 records

Show feature table

Start	End	DB	Term	Name
158	182	ProSitePatterns	PS00963	Ribosomal protein S2 signature 2.
158	182	InterPro	IPR018130	Ribosomal protein S2, conserved site
3	226	NCBIfam	TIGR01011	30S ribosomal protein S2
3	226	InterPro	IPR005706	Ribosomal protein S2, bacteria/mitochondria/plastid
6	17	ProSitePatterns	PS00962	Ribosomal protein S2 signature 1.
6	17	InterPro	IPR018130	Ribosomal protein S2, conserved site
2	225	Hamap	MF_00291_B	30S ribosomal protein S2 [rpsB].
2	225	InterPro	IPR005706	Ribosomal protein S2, bacteria/mitochondria/plastid
9	224	Pfam	PF00318	Ribosomal protein S2
9	224	InterPro	IPR001865	Ribosomal protein S2
105	150	Gene3D	G3DSA:1.10.287.610	Helix hairpin bin
196	210	PRINTS	PR00395	Ribosomal protein S2 signature
196	210	InterPro	IPR001865	Ribosomal protein S2
37	46	PRINTS	PR00395	Ribosomal protein S2 signature
37	46	InterPro	IPR001865	Ribosomal protein S2
175	186	PRINTS	PR00395	Ribosomal protein S2 signature
175	186	InterPro	IPR001865	Ribosomal protein S2
87	104	PRINTS	PR00395	Ribosomal protein S2 signature
87	104	InterPro	IPR001865	Ribosomal protein S2
158	175	PRINTS	PR00395	Ribosomal protein S2 signature
158	175	InterPro	IPR001865	Ribosomal protein S2
6	24	PRINTS	PR00395	Ribosomal protein S2 signature
6	24	InterPro	IPR001865	Ribosomal protein S2
102	151	FunFam	G3DSA:1.10.287.610:FF:000001	30S ribosomal protein S2
6	235	SUPERFAMILY	SSF52313	Ribosomal protein S2
6	235	InterPro	IPR023591	Ribosomal protein S2, flavodoxin-like domain superfamily
9	223	CDD	cd01425	RPS2
9	223	InterPro	IPR001865	Ribosomal protein S2
7	241	Gene3D	G3DSA:3.40.50.10490	-
2	236	PANTHER	PTHR12534	30S RIBOSOMAL PROTEIN S2 PROKARYOTIC AND ORGANELLAR
2	236	InterPro	IPR005706	Ribosomal protein S2, bacteria/mitochondria/plastid

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_A0A0H3GS30	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01811	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
15				0.332

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				0.7
9				0.332
5				0.29
14				0.225

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				2.41	0.065

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.

52 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
TAC	1I97	P80371	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`C[C@]1(c2cccc(c2C(=O)C3=C([C@]4([C@@H](C[C@@H]3…`
WO2	1I94	P80371	—	—	—	`[O][W]1234O[W]567(O[W]89%10(O5[P]5%11O%12[W]%13…`

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
ZINC11525121	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC18202167	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC20410403	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC21984166	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC239173596	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC4059755	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC4215819	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3C…`
ZINC43771554	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC4807269	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC575338663	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C(…`
ZINC84441937	1.000	444.4 Da LogP -0.21 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC28630683	0.800	444.4 Da LogP 0.84 TPSA 182.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(=N)O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC35051264	0.800	444.4 Da LogP 0.84 TPSA 182.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(=N)O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC71769623	0.793	417.4 Da LogP -0.78 TPSA 198.6	1 viol.	✓ Clean	`C[C@@]1(O)c2cccc(O)c2C(=O)C2=C(O)[C@]3(O)C(=O)C…`
ZINC71769624	0.793	417.4 Da LogP -0.78 TPSA 198.6	1 viol.	✓ Clean	`C[C@@]1(O)c2cccc(O)c2C(=O)C2=C(O)[C@]3(O)C(=O)C…`
ZINC71769638	0.793	416.4 Da LogP -0.82 TPSA 204.4	1 viol.	✓ Clean	`C[C@@]1(O)c2cccc(O)c2C(=O)C2=C(O)[C@]3(O)C(=O)C…`
ZINC14768423	0.762	478.9 Da LogP 0.44 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC19701767	0.762	478.9 Da LogP 0.44 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC19701769	0.762	478.9 Da LogP 0.44 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC22054932	0.762	478.9 Da LogP 0.44 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3C…`
ZINC34800280	0.762	478.9 Da LogP 0.44 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC35024403	0.762	478.9 Da LogP 0.44 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC43769566	0.762	478.9 Da LogP 0.44 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC44019569	0.762	478.9 Da LogP 0.44 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C(…`
ZINC44830179	0.762	478.9 Da LogP 0.44 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC71789581	0.762	478.9 Da LogP 0.44 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC86860183	0.762	478.9 Da LogP 0.44 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C(…`
ZINC13736610	0.754	459.5 Da LogP -0.07 TPSA 178.4	1 viol.	✓ Clean	`C[C@@]1(O)c2cccc(O)c2C(=O)C2=C(O)[C@]3(O)C(=O)C…`
ZINC2382315467	0.698	430.4 Da LogP -0.39 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC4215546	0.698	430.4 Da LogP -0.39 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC4879577	0.689	401.4 Da LogP 0.25 TPSA 178.4	1 viol.	✓ Clean	`C[C@]1(O)c2cccc(O)c2C(=O)C2=C(O)[C@@]3(O)C(=O)C…`
ZINC4879578	0.689	401.4 Da LogP 0.25 TPSA 178.4	1 viol.	✓ Clean	`C[C@@]1(O)c2cccc(O)c2C(=O)C2=C(O)[C@@]3(O)C(=O)…`
ZINC4879581	0.689	401.4 Da LogP 0.25 TPSA 178.4	1 viol.	✓ Clean	`C[C@]1(O)c2cccc(O)c2C(=O)C2=C(O)[C@]3(O)C(=O)C(…`
ZINC4879584	0.689	401.4 Da LogP 0.25 TPSA 178.4	1 viol.	✓ Clean	`C[C@@]1(O)c2cccc(O)c2C(=O)C2=C(O)[C@]3(O)C(=O)C…`
ZINC59402062	0.689	401.4 Da LogP 0.25 TPSA 178.4	1 viol.	✓ Clean	`C[C@@]1(O)c2cccc(O)c2C(=O)C2=C(O)[C@]3(O)C(=O)C…`
ZINC100303069	0.688	444.4 Da LogP -0.37 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(=O)C(C(N)=O)=C(O)[C@@]2(O)C(=O)C3…`
ZINC198562282	0.688	444.4 Da LogP -0.37 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(=O)C(C(N)=O)=C(O)[C@]2(O)C(=O)C3=…`
ZINC198562314	0.688	444.4 Da LogP -0.37 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(=O)C(C(N)=O)=C(O)[C@]2(O)C(=O)C3=…`
ZINC198633879	0.688	444.4 Da LogP -0.37 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@H]1C(=O)C(C(N)=O)=C(O)[C@@]2(O)C(=O)C3=…`
ZINC199057634	0.688	444.4 Da LogP -0.37 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(=O)C(C(N)=O)=C(O)[C@]2(O)C(=O)C3=…`
ZINC199362416	0.688	444.4 Da LogP -0.37 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C@@H]1C(=O)C(C(N)=O)=C(O)[C@]2(O)C(=O)C3=…`
ZINC22066481	0.688	414.4 Da LogP 0.12 TPSA 161.4	✓ Ro5	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC306122643	0.688	414.4 Da LogP 0.12 TPSA 161.4	✓ Ro5	✓ Clean	`CN(C)[C@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C(…`
ZINC59364526	0.688	414.4 Da LogP 0.12 TPSA 161.4	✓ Ro5	✓ Clean	`CN(C)[C@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3C…`
ZINC59364527	0.688	414.4 Da LogP 0.12 TPSA 161.4	✓ Ro5	✓ Clean	`CN(C)[C@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3C…`
ZINC59364530	0.688	414.4 Da LogP 0.12 TPSA 161.4	✓ Ro5	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3…`
ZINC1560410656	0.683	443.4 Da LogP -0.05 TPSA 181.6	1 viol.	✓ Clean	`CN(C)[C]1C(O)=C(C(N)=O)C(=O)[C@@]2(O)C(O)=C3C(=…`
ZINC13783188	0.677	460.4 Da LogP -1.24 TPSA 201.8	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC35947013	0.677	460.4 Da LogP -1.24 TPSA 201.8	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`
ZINC36384720	0.677	460.4 Da LogP -1.24 TPSA 201.8	1 viol.	✓ Clean	`CN(C)[C@@H]1C(O)=C(C(N)=O)C(=O)[C@]2(O)C(O)=C3C…`

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.