Protein profile

KP13_00755

30S ribosomal protein S3

Genome: KpKP13

Gene: rpsC AHE42371.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GU21

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Amino acids 232

Annotations 7

Features 26

PDB binders 7

Druggability 0.439

Overview

Basic information about this protein and its source genome.

Accession: KP13_00755
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rpsC AHE42371.1
Status: annotated
Amino acids: 232
Structure source: AlphaFold + ColabFold

GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0003676 Binding to a nucleic acid. 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: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. GO:0003729 Binding to messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 28.652
Human E-value: 1.94e-06
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 99.142
DEG E-value: 6.72e-169
Localization: Cytoplasmic
ColabFold pLDDT: 88.5

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 0.439

Structure A0A0H3GU21

Pocket Pocket 1

P2Rank 0.514

Structure A0A0H3GU21

Pocket Pocket 1

ColabFold model

FPocket 0.346 · Pocket 10

P2Rank 0.697 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 3421 / 4744 genomes with a hit

Normalized 0.721

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0003676 Binding to a nucleic acid.
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: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.
GO:0003729 Binding to messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
GO:0019843 Binding to a ribosomal RNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records

Show feature table

Start	End	DB	Term	Name
109	232	Gene3D	G3DSA:3.30.1140.32	-
109	232	InterPro	IPR036419	Ribosomal protein S3, C-terminal domain superfamily
1	209	NCBIfam	TIGR01009	30S ribosomal protein S3
1	209	InterPro	IPR005704	Ribosomal protein S3, bacterial-type
163	197	ProSitePatterns	PS00548	Ribosomal protein S3 signature.
163	197	InterPro	IPR018280	Ribosomal protein S3, conserved site
60	125	SMART	SM00322	kh_6
60	125	InterPro	IPR004087	K Homology domain
13	212	PANTHER	PTHR11760	30S/40S RIBOSOMAL PROTEIN S3
120	202	Pfam	PF00189	Ribosomal protein S3, C-terminal domain
120	202	InterPro	IPR001351	Ribosomal protein S3, C-terminal
2	106	SUPERFAMILY	SSF54814	Prokaryotic type KH domain (KH-domain type II)
2	106	InterPro	IPR009019	K homology domain superfamily, prokaryotic type
17	107	Gene3D	G3DSA:3.30.300.20	-
17	107	InterPro	IPR015946	K homology domain-like, alpha/beta
38	111	Pfam	PF07650	KH domain
38	111	InterPro	IPR004044	K Homology domain, type 2
109	230	FunFam	G3DSA:3.30.1140.32:FF:000001	30S ribosomal protein S3
108	206	SUPERFAMILY	SSF54821	Ribosomal protein S3 C-terminal domain
108	206	InterPro	IPR036419	Ribosomal protein S3, C-terminal domain superfamily
17	107	FunFam	G3DSA:3.30.300.20:FF:000001	30S ribosomal protein S3
2	109	CDD	cd02412	KH-II_30S_S3
39	107	ProSiteProfiles	PS50823	Type-2 KH domain profile.
39	107	InterPro	IPR004044	K Homology domain, type 2
1	206	Hamap	MF_01309_B	30S ribosomal protein S3 [rpsC].
1	206	InterPro	IPR005704	Ribosomal protein S3, bacterial-type

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_A0A0H3GU21	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00755	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
1				0.439

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				5.95	0.292

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
10				0.346

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	Score	Probability
1	8.65	0.462
2	1.19	0.01
3	1.05	0.006

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.

57 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
4D4	5IT8	P0A7V3	190.2 Da LogP -2.37 TPSA 145.4	1 viol.	✓ Clean	`[H]/N=C(/N)\NCC[C@H]([C@@H](C(=O)O)N)O`
GCP	5LZW	G1TNM3	521.2 Da LogP -2.22 TPSA 289.9	3 viol.	✓ Clean	`c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…`
GUN	4YBB	P0A7V3	151.1 Da LogP -0.77 TPSA 100.5	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)C(=O)NC(=N2)N`
MEQ	5J7L	P0A7V3	160.2 Da LogP -1.08 TPSA 92.4	✓ Ro5	✓ Clean	`CNC(=O)CC[C@@H](C(=O)O)N`
PUT	4YBB	P0A7V3	88.2 Da LogP -0.32 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CN`
TAC	5J7L	P0A7V3	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	P80372	—	—	—	`[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…`
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`
ZINC104869865	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O…`
ZINC12504289	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC34541308	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC35000839	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC45284491	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC80639694	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
ZINC8215481	0.850	443.2 Da LogP -2.45 TPSA 252.6	2 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(…`
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…`
ZINC1529737	0.714	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC2384790	0.714	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC2560745	0.714	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC2560989	0.714	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
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…`
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(…`

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.