Protein profile

VK055_3777

ribosomal protein S4

Genome: KpATCC43816

Gene: AIK82332.1 rpsD Structure source: AlphaFold + ColabFold UniProt A0A0H3GWI6
Amino acids 206
Annotations 6
Features 23
PDB binders 28
Druggability 0.803

Overview

Basic information about this protein and its source genome.

Accession
VK055_3777
Gene
AIK82332.1 rpsD
Status
annotated
Amino acids
206
Structure source
AlphaFold + ColabFold

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 (%)
98.058
DEG E-value
1.57e-149
Localization
Cytoplasmic
ColabFold pLDDT
93.14

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 0.803
Structure A0A0H3GWI6
Pocket Pocket 1
P2Rank 0.458
Structure A0A0H3GWI6
Pocket Pocket 1
ColabFold model
FPocket 0.693 · Pocket 1
P2Rank 0.371 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 2312 / 4744 genomes with a hit
Normalized 0.487

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.
  • GO:0015935 The smaller of the two subunits of a ribosome.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • 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:0019843 Binding to a ribosomal RNA.
  • GO:0042274 A cellular process that results in the biosynthesis of constituent macromolecules, assembly, and arrangement of constituent parts of a small ribosomal subunit; includes transport to the sites of protein synthesis.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
95 191 Gene3D G3DSA:3.10.290.10 -
95 191 InterPro IPR036986 RNA-binding S4 domain superfamily
28 179 PANTHER PTHR11831 30S 40S RIBOSOMAL PROTEIN
28 179 InterPro IPR022801 Ribosomal protein S4/S9
3 206 NCBIfam TIGR01017 30S ribosomal protein S4
3 206 InterPro IPR005709 Ribosomal protein S4, bacterial-type
3 206 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif
1 206 Hamap MF_01306_B 30S ribosomal protein S4 [rpsD].
1 206 InterPro IPR005709 Ribosomal protein S4, bacterial-type
94 118 ProSitePatterns PS00632 Ribosomal protein S4 signature.
94 118 InterPro IPR018079 Ribosomal protein S4, conserved site
3 103 FunFam G3DSA:1.10.1050.10:FF:000001 30S ribosomal protein S4
95 191 FunFam G3DSA:3.10.290.10:FF:000001 30S ribosomal protein S4
97 143 Pfam PF01479 S4 domain
97 143 InterPro IPR002942 RNA-binding S4 domain
97 156 CDD cd00165 S4
96 160 SMART SM00363 s4_6
96 160 InterPro IPR002942 RNA-binding S4 domain
3 95 SMART SM01390 Ribosomal_S4_2
3 95 InterPro IPR001912 Ribosomal protein S4/S9, N-terminal
3 95 Pfam PF00163 Ribosomal protein S4/S9 N-terminal domain
3 206 Gene3D G3DSA:1.10.1050.10 Ribosomal Protein S4 Delta 41; Chain A, domain 1
96 156 ProSiteProfiles PS50889 S4 RNA-binding domain profile.

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

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_A0A0H3GWI6
AlphaFold full sequence Viewing
ColabFold VK055_3777
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 0.803
2 0.453

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 7.4 0.387

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.

78 records

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
004 P80373 151.2 Da LogP 0.77 TPSA 63.3 ✓ Ro5 ✓ Clean c1ccc(cc1)[C@@H](C(=O)O)N
2QZ P80373 147.2 Da LogP -0.62 TPSA 60.8 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C(=O)O)N(C)C)O
2R1 P80373 159.1 Da LogP -1.33 TPSA 96.1 ✓ Ro5 ✓ Clean C1[C@H](O1)/C(=C(\C(=O)O)/N)/CO
2R3 P80373 211.2 Da LogP 0.14 TPSA 92.8 ✓ Ro5 ✓ Clean COc1ccc(cc1)[C@H]([C@@H](C(=O)O)N)O
5MC P80373 337.2 Da LogP -2.14 TPSA 177.4 ✓ Ro5 ✓ Clean CC1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)…
5MU P80373 338.2 Da LogP -2.43 TPSA 171.3 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
7MG P80373 379.3 Da LogP -2.88 TPSA 194.7 1 viol. ✓ Clean CN1CN(C2=C1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H]([C…
9VA P80373 199.2 Da LogP -1.82 TPSA 104.8 ✓ Ro5 ✓ Clean C1=N[C@H](C(=O)N[C@H]1CCC(=O)N)CO
A P80373 347.2 Da LogP -1.86 TPSA 186.1 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
A2M P80373 361.3 Da LogP -1.21 TPSA 175.1 ✓ Ro5 ✓ Clean CO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2ncnc3N)COP…
A3P P80373 427.2 Da LogP -1.75 TPSA 232.6 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
C P80373 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…
FSD P80373 618.7 Da LogP -0.38 TPSA 210.7 3 viol. ✓ Clean C[C@@H]1[C@H](CC[C@@H](O1)N2C=CC(=NC2=O)NC(=O)c…
FUA P80373 516.7 Da LogP 5.67 TPSA 104.1 2 viol. ✓ Clean C[C@H]1[C@@H]2CC[C@]3([C@H]([C@]2(CC[C@H]1O)C)[…
G7M P80373 378.3 Da LogP -3.14 TPSA 197.0 1 viol. ✓ Clean C[n+]1cn(c2c1C(=O)NC(=N2)N)[C@H]3[C@@H]([C@@H](…
GCP P80373 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…
LUJ P80373 641.7 Da LogP -6.81 TPSA 327.1 3 viol. ✓ Clean CCC[C@@H]1[C@H](O[C@@H]([C@@H]([C@H]1O)N)O[C@@H…
M2G P80373 391.3 Da LogP -2.09 TPSA 183.3 ✓ Ro5 ✓ Clean CN(C)C1=Nc2c(ncn2[C@H]3[C@@H]([C@@H]([C@H](O3)C…
MVA P80373 131.2 Da LogP 0.31 TPSA 49.3 ✓ Ro5 ✓ Clean CC(C)[C@@H](C(=O)O)NC
NMY P80373 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@…
OHX P80373 286.4 Da LogP -3.55 TPSA 156.1 1 viol. ✓ Clean N[Os](N)(N)(N)(N)N
OMG P80373 377.3 Da LogP -1.92 TPSA 195.0 ✓ Ro5 ✓ Clean CO[C@@H]1[C@@H]([C@H](O[C@H]1n2cnc3c2N=C(NC3=O)…
OMU P80373 338.2 Da LogP -2.08 TPSA 160.3 ✓ Ro5 ✓ Clean CO[C@@H]1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO…
PAR P80373 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@…
PCY P80373 558.6 Da LogP 0.75 TPSA 194.7 2 viol. ✓ Clean Cc1cccc(c1C(=O)OC[C@]2([C@H]([C@@H]([C@]([C@@]2…
PSU P80373 324.2 Da LogP -2.67 TPSA 182.2 1 viol. ✓ Clean C1=C(C(=O)NC(=O)N1)[C@H]2[C@@H]([C@@H]([C@H](O2…
TAC P80373 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 P80373 [O][W]1234O[W]567(O[W]89%10(O5[P]5%11O%12[W]%13…

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.