Protein profile

KP13_00766

30S ribosomal protein S5

Genome: KpKP13

Gene: rpsE AHE42380.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H3V5

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Amino acids 167

Annotations 5

Features 21

PDB binders 10

Druggability 0.26

Overview

Basic information about this protein and its source genome.

Accession: KP13_00766
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rpsE AHE42380.1
Status: annotated
Amino acids: 167
Structure source: AlphaFold + ColabFold

GO:0015935 The smaller of the two subunits of a ribosome. GO:0003735 The action of a molecule that contributes to the structural integrity of the 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:0003723 Binding to an RNA molecule or a portion thereof. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 29.197
Human E-value: 4.6e-08
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 97.006
DEG E-value: 1.2599999999999998e-115
Localization: Cytoplasmic
ColabFold pLDDT: 90.5

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 0.26

Structure A0A0H3H3V5

Pocket Pocket 1

P2Rank 0.053

Structure A0A0H3H3V5

Pocket Pocket 1

ColabFold model

FPocket 0.339 · Pocket 4

P2Rank 0.024 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 2710 / 4744 genomes with a hit

Normalized 0.571

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:0003735 The action of a molecule that contributes to the structural integrity of the 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:0003723 Binding to an RNA molecule or a portion thereof.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
11	74	ProSiteProfiles	PS50881	S5 double stranded RNA-binding domain profile.
11	74	InterPro	IPR013810	Ribosomal protein S5, N-terminal
10	163	PANTHER	PTHR48277	MITOCHONDRIAL RIBOSOMAL PROTEIN S5
10	163	InterPro	IPR000851	Ribosomal protein S5
75	166	FunFam	G3DSA:3.30.230.10:FF:000002	30S ribosomal protein S5
1	72	FunFam	G3DSA:3.30.160.20:FF:000001	30S ribosomal protein S5
74	167	Gene3D	G3DSA:3.30.230.10	-
74	167	InterPro	IPR014721	Ribosomal protein S5 domain 2-type fold, subgroup
87	157	Pfam	PF03719	Ribosomal protein S5, C-terminal domain
87	157	InterPro	IPR005324	Ribosomal protein S5, C-terminal
9	75	SUPERFAMILY	SSF54768	dsRNA-binding domain-like
10	163	NCBIfam	TIGR01021	30S ribosomal protein S5
10	163	InterPro	IPR005712	Ribosomal protein S5, bacterial-type
1	73	Gene3D	G3DSA:3.30.160.20	-
11	74	Pfam	PF00333	Ribosomal protein S5, N-terminal domain
1	163	Hamap	MF_01307_B	30S ribosomal protein S5 [rpsE].
1	163	InterPro	IPR005712	Ribosomal protein S5, bacterial-type
28	60	ProSitePatterns	PS00585	Ribosomal protein S5 signature.
28	60	InterPro	IPR018192	Ribosomal protein S5, N-terminal, conserved site
79	159	SUPERFAMILY	SSF54211	Ribosomal protein S5 domain 2-like
79	159	InterPro	IPR020568	Ribosomal protein S5 domain 2-type fold

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_A0A0H3H3V5	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00766	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				0.26

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				1.3	0.014

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
4				0.339
9				0.258

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.

60 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
C	6CAO	Q5SHQ5	323.2 Da LogP -2.45 TPSA 177.4	✓ Ro5	✓ Clean	`C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`
GCP	4V8Y	P25443	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…`
MEQ	5J7L	P0A7W1	160.2 Da LogP -1.08 TPSA 92.4	✓ Ro5	✓ Clean	`CNC(=O)CC[C@@H](C(=O)O)N`
OHX	4V8Y	P25443	286.4 Da LogP -3.55 TPSA 156.1	1 viol.	✓ Clean	`N[Os](N)(N)(N)(N)N`
PAR	4X62	Q5SHQ5	615.6 Da LogP -8.86 TPSA 347.3	3 viol.	✓ Clean	`C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…`
PUT	5J7L	P0A7W1	88.2 Da LogP -0.32 TPSA 52.0	✓ Ro5	✓ Clean	`C(CCN)CN`
SCM	4V56	P0A7W1	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`C[C@@H]1CC(=O)[C@]2([C@@H](O1)O[C@@H]3[C@H]([C@…`
SRY	1FJG	Q5SHQ5	581.6 Da LogP -7.74 TPSA 331.4	3 viol.	✓ Clean	`[H]/N=C(/N)\N[C@@H]1[C@H]([C@@H]([C@H]([C@@H]([…`
TAC	5J7L	P0A7W1	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	1DV4	P02357	—	—	—	`[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…`
ZINC245256945	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](NC)[C@@H](O)[C@H]2O[C@H…`
ZINC245256946	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@@H]1[C@@H]2O[C@]3(O)C(=O)C[C@H](C)O[C@@H]3…`
ZINC245256947	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@@H]1[C@@H]2O[C@]3(O)C(=O)C[C@H](C)O[C@@H]3…`
ZINC245256948	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](NC)[C@H](O)[C@H]2O[C@H]…`
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…`
ZINC5273778	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H]2O[C@H]3O[C@@H](C)CC(=O…`
ZINC53006806	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](NC)[C@H](O)[C@H]2O[C@@H…`
ZINC57406608	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](NC)[C@@H](O)[C@H]2O[C@@…`
ZINC57406609	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](NC)[C@@H](O)[C@H]2O[C@@…`
ZINC57406610	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](NC)[C@@H](O)[C@H]2O[C@@…`
ZINC57406611	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](NC)[C@@H](O)[C@H]2O[C@@…`
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(…`
ZINC71789713	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@@H]1[C@H](O)[C@H]2O[C@@H]3O[C@@H](C)CC(=O)…`
ZINC71789714	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@@H]1[C@H](O)[C@H]2O[C@H]3O[C@@H](C)CC(=O)[…`
ZINC71789715	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@@H]1[C@H](O)[C@H]2O[C@@H]3O[C@@H](C)CC(=O)…`
ZINC71789716	1.000	332.4 Da LogP -2.93 TPSA 129.5	✓ Ro5	✓ Clean	`CN[C@@H]1[C@H](O)[C@H]2O[C@H]3O[C@@H](C)CC(=O)[…`
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…`
ZINC100052153	0.905	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	0.905	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	0.905	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	0.905	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	0.905	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	0.905	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	0.905	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	0.905	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	0.905	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	0.905	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	0.905	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	0.905	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	0.905	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]…`
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`
ZINC60184027	0.810	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](…`
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…`
ZINC12501413	0.783	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC2159505	0.783	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)…`
ZINC9334496	0.783	363.2 Da LogP -2.57 TPSA 206.0	1 viol.	✓ Clean	`Nc1nc2c(ncn2[C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[…`

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.