Protein profile

KP13_04198

30S ribosomal protein S1

Genome: KpKP13

Gene: AHE45429.1 rpsA Structure source: AlphaFold + ColabFold UniProt A0A0H3GQZ9

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Amino acids 557

Annotations 7

Features 95

PDB binders 1

Druggability 0.565

Overview

Basic information about this protein and its source genome.

Accession: KP13_04198
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45429.1 rpsA
Status: annotated
Amino acids: 557
Structure source: AlphaFold + ColabFold

GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome. 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: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. 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 (%): 46.032
Human E-value: 7.27e-08
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 98.923
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 69.72

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 0.565

Structure A0A0H3GQZ9

Pocket Pocket 34

P2Rank

Structure A0A0H3GQZ9

Pocket No pockets

ColabFold model

FPocket 0.334 · Pocket 1

P2Rank 0.004 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 281 / 4744 genomes with a hit

Normalized 0.059

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.
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: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.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

95 records

Show feature table

Start	End	DB	Term	Name
225	259	ProSiteProfiles	PS50889	S4 RNA-binding domain profile.
1	534	PIRSF	PIRSF002111	RpsA
1	534	InterPro	IPR000110	Ribosomal protein S1
275	347	SMART	SM00316	S1_6
275	347	InterPro	IPR022967	RNA-binding domain, S1
19	87	SMART	SM00316	S1_6
19	87	InterPro	IPR022967	RNA-binding domain, S1
362	434	SMART	SM00316	S1_6
362	434	InterPro	IPR022967	RNA-binding domain, S1
449	520	SMART	SM00316	S1_6
449	520	InterPro	IPR022967	RNA-binding domain, S1
103	171	SMART	SM00316	S1_6
103	171	InterPro	IPR022967	RNA-binding domain, S1
190	260	SMART	SM00316	S1_6
190	260	InterPro	IPR022967	RNA-binding domain, S1
270	357	FunFam	G3DSA:2.40.50.140:FF:000011	30S ribosomal protein S1
1	112	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
1	112	InterPro	IPR012340	Nucleic acid-binding, OB-fold
445	528	FunFam	G3DSA:2.40.50.140:FF:000036	30S ribosomal protein S1
189	277	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
189	277	InterPro	IPR012340	Nucleic acid-binding, OB-fold
21	87	CDD	cd05687	S1_RPS1_repeat_ec1_hs1
183	267	FunFam	G3DSA:2.40.50.140:FF:000018	30S ribosomal protein S1
192	260	ProSiteProfiles	PS50126	S1 domain profile.
192	260	InterPro	IPR003029	S1 domain
255	370	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
255	370	InterPro	IPR012340	Nucleic acid-binding, OB-fold
364	432	CDD	cd05690	S1_RPS1_repeat_ec5
364	434	ProSiteProfiles	PS50126	S1 domain profile.
364	434	InterPro	IPR003029	S1 domain
106	185	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
106	185	InterPro	IPR012340	Nucleic acid-binding, OB-fold
277	347	ProSiteProfiles	PS50126	S1 domain profile.
277	347	InterPro	IPR003029	S1 domain
362	443	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
362	443	InterPro	IPR012340	Nucleic acid-binding, OB-fold
451	523	CDD	cd05691	S1_RPS1_repeat_ec6
429	536	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
429	536	InterPro	IPR012340	Nucleic acid-binding, OB-fold
451	520	ProSiteProfiles	PS50126	S1 domain profile.
451	520	InterPro	IPR003029	S1 domain
6	97	Gene3D	G3DSA:2.40.50.140	-
6	97	InterPro	IPR012340	Nucleic acid-binding, OB-fold
444	528	Gene3D	G3DSA:2.40.50.140	-
444	528	InterPro	IPR012340	Nucleic acid-binding, OB-fold
182	265	Gene3D	G3DSA:2.40.50.140	-
182	265	InterPro	IPR012340	Nucleic acid-binding, OB-fold
106	171	CDD	cd04465	S1_RPS1_repeat_ec2_hs2
358	444	FunFam	G3DSA:2.40.50.140:FF:000016	30S ribosomal protein S1
6	97	FunFam	G3DSA:2.40.50.140:FF:000021	30S ribosomal protein S1
21	87	ProSiteProfiles	PS50126	S1 domain profile.
21	87	InterPro	IPR003029	S1 domain
155	175	PRINTS	PR00681	Ribosomal protein S1 signature
155	175	InterPro	IPR035104	Ribosomal protein S1-like
330	348	PRINTS	PR00681	Ribosomal protein S1 signature
330	348	InterPro	IPR035104	Ribosomal protein S1-like
21	39	PRINTS	PR00681	Ribosomal protein S1 signature
21	39	InterPro	IPR035104	Ribosomal protein S1-like
126	143	PRINTS	PR00681	Ribosomal protein S1 signature
126	143	InterPro	IPR035104	Ribosomal protein S1-like
212	233	PRINTS	PR00681	Ribosomal protein S1 signature
212	233	InterPro	IPR035104	Ribosomal protein S1-like
290	309	PRINTS	PR00681	Ribosomal protein S1 signature
290	309	InterPro	IPR035104	Ribosomal protein S1-like
39	53	PRINTS	PR00681	Ribosomal protein S1 signature
39	53	InterPro	IPR035104	Ribosomal protein S1-like
108	124	PRINTS	PR00681	Ribosomal protein S1 signature
108	124	InterPro	IPR035104	Ribosomal protein S1-like
84	103	PRINTS	PR00681	Ribosomal protein S1 signature
84	103	InterPro	IPR035104	Ribosomal protein S1-like
98	181	FunFam	G3DSA:2.40.50.140:FF:000017	30S ribosomal protein S1
19	78	Pfam	PF00575	S1 RNA binding domain
19	78	InterPro	IPR003029	S1 domain
449	520	Pfam	PF00575	S1 RNA binding domain
449	520	InterPro	IPR003029	S1 domain
361	434	Pfam	PF00575	S1 RNA binding domain
361	434	InterPro	IPR003029	S1 domain
190	260	Pfam	PF00575	S1 RNA binding domain
190	260	InterPro	IPR003029	S1 domain
275	347	Pfam	PF00575	S1 RNA binding domain
275	347	InterPro	IPR003029	S1 domain
104	171	Pfam	PF00575	S1 RNA binding domain
104	171	InterPro	IPR003029	S1 domain
3	520	NCBIfam	TIGR00717	30S ribosomal protein S1
3	520	InterPro	IPR000110	Ribosomal protein S1
267	357	Gene3D	G3DSA:2.40.50.140	-
267	357	InterPro	IPR012340	Nucleic acid-binding, OB-fold
358	443	Gene3D	G3DSA:2.40.50.140	-
358	443	InterPro	IPR012340	Nucleic acid-binding, OB-fold
98	181	Gene3D	G3DSA:2.40.50.140	-
98	181	InterPro	IPR012340	Nucleic acid-binding, OB-fold
363	442	PANTHER	PTHR10724	30S RIBOSOMAL PROTEIN S1
105	171	ProSiteProfiles	PS50126	S1 domain profile.
105	171	InterPro	IPR003029	S1 domain
191	258	CDD	cd05688	S1_RPS1_repeat_ec3

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_A0A0H3GQZ9	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04198	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
34				0.565
1				0.007
39				0.001
28				0.0

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
26				0.026
2				0.003
8				0.002
25				0.0

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				0.9	0.004

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.

39 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
VGL	4NNI	P9WH43	124.1 Da LogP 0.17 TPSA 63.1	✓ Ro5	✓ Clean	`c1cnc(cn1)C(=O)O`

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DXH	Q14690	7.47	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cnn(c3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
DWT	Q14690	7.14	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`

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
ZINC20357720	0.581	228.2 Da LogP 1.41 TPSA 80.1	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1cnccn1`
ZINC2749775	0.552	272.3 Da LogP -0.57 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)c1cnccn1)c1cnccn1`
ZINC20496347	0.548	219.3 Da LogP 1.88 TPSA 46.1	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCCCCCC1`
ZINC5705248	0.548	205.3 Da LogP 1.49 TPSA 46.1	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCCCCC1`
ZINC69048726	0.548	201.2 Da LogP 1.24 TPSA 76.0	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2cnccn2)cn1`
ZINC12360654	0.545	207.2 Da LogP 1.30 TPSA 76.0	✓ Ro5	✓ Clean	`O=C(O)c1csc(-c2cnccn2)n1`
ZINC26423456	0.543	250.2 Da LogP 0.88 TPSA 105.1	✓ Ro5	✓ Clean	`O=C(O)c1csc(NC(=O)c2cnccn2)n1`
ZINC220133900	0.538	398.3 Da LogP 3.77 TPSA 85.1	✓ Ro5	✓ Clean	`Cc1nc2nc(-c3cccnc3)nn2cc1C(=O)Nc1cccc(C(F)(F)F)…`
ZINC20148987	0.532	414.4 Da LogP 4.50 TPSA 97.1	✓ Ro5	✓ Clean	`Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1Nc1cncc(C(N)…`
ZINC2580774	0.531	216.3 Da LogP 2.41 TPSA 42.9	✓ Ro5	✓ Clean	`O=C(Sc1ccccc1)c1cnccn1`
ZINC4749098	0.529	243.2 Da LogP 1.43 TPSA 92.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2cnccn2)cc1`
ZINC2747329	0.516	300.3 Da LogP 0.21 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NCCCCNC(=O)c1cnccn1)c1cnccn1`
ZINC2747452	0.516	286.3 Da LogP -0.18 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NCCCNC(=O)c1cnccn1)c1cnccn1`
ZINC19092783	0.515	205.2 Da LogP 0.28 TPSA 63.2	✓ Ro5	✓ Clean	`O=C1CCN(C(=O)c2cnccn2)CC1`
ZINC40542019	0.515	209.3 Da LogP 0.67 TPSA 46.1	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCSCC1`
ZINC54792854	0.515	202.2 Da LogP 0.63 TPSA 88.9	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2cnccn2)n1`
ZINC74212868	0.515	201.2 Da LogP 1.24 TPSA 76.0	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2cnccn2)n1`
ZINC79435988	0.515	209.2 Da LogP -0.32 TPSA 83.4	✓ Ro5	✓ Clean	`CN(CC(=O)O)CC(=O)c1cnccn1`
ZINC96047318	0.515	366.4 Da LogP 1.43 TPSA 92.2	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCC2(CC1)CCN(C(=O)c1cnccn1)CC2`
ZINC21953682	0.514	235.2 Da LogP 0.41 TPSA 83.4	✓ Ro5	✓ Clean	`O=C(O)C1CCN(C(=O)c2cnccn2)CC1`
ZINC9306398	0.512	398.3 Da LogP 3.77 TPSA 85.1	✓ Ro5	✓ Clean	`Cc1c(C(=O)Nc2cccc(C(F)(F)F)c2)cnc2nc(-c3cccnc3)…`
ZINC5049572	0.507	336.3 Da LogP 4.22 TPSA 58.2	✓ Ro5	✓ Clean	`CC(=O)Nc1cc(C(=O)Nc2cccc(C(F)(F)F)c2)ccc1C`
ZINC72174470	0.507	360.4 Da LogP 2.73 TPSA 93.4	✓ Ro5	✓ Clean	`Cn1ncc2c(NCCCNc3cccnc3)nc(-c3cccnc3)nc21`
ZINC72149792	0.506	360.4 Da LogP 2.65 TPSA 93.4	✓ Ro5	✓ Clean	`Cc1cnccc1NCCNc1nc(-c2cccnc2)nc2c1cnn2C`
ZINC12982005	0.500	221.2 Da LogP 0.17 TPSA 83.4	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1CCCN1C(=O)c1cnccn1`
ZINC13208295	0.500	200.2 Da LogP 1.12 TPSA 67.8	✓ Ro5	✓ Clean	`O=C(Nc1ccncc1)c1cnccn1`
ZINC20280834	0.500	221.2 Da LogP 0.17 TPSA 83.4	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CCCN1C(=O)c1cnccn1`
ZINC2755537	0.500	328.4 Da LogP 0.99 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NCCCCCCNC(=O)c1cnccn1)c1cnccn1`
ZINC32004931	0.500	202.2 Da LogP 1.85 TPSA 42.9	✓ Ro5	✓ Clean	`O=C(c1ccc(F)cc1)c1cnccn1`
ZINC35110503	0.500	207.2 Da LogP 0.07 TPSA 66.3	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCC(O)CC1`
ZINC375500	0.500	326.4 Da LogP 0.74 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NC1CCC(NC(=O)c2cnccn2)CC1)c1cnccn1`
ZINC37658100	0.500	218.6 Da LogP 2.36 TPSA 42.9	✓ Ro5	✓ Clean	`O=C(c1ccc(Cl)cc1)c1cnccn1`
ZINC54856994	0.500	202.2 Da LogP 0.63 TPSA 88.9	✓ Ro5	✓ Clean	`O=C(O)c1cnc(-c2cnccn2)nc1`
ZINC646774339	0.500	231.3 Da LogP 1.74 TPSA 46.1	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCC(C2CC2)CC1`
ZINC77101491	0.500	207.2 Da LogP -0.37 TPSA 83.4	✓ Ro5	✓ Clean	`O=C(O)C1CN(C(=O)c2cnccn2)C1`
ZINC96053972	0.500	324.3 Da LogP 0.11 TPSA 92.2	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CC2CN(C(=O)c3cnccn3)CC2C1`

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.