KpKP13 Protein target profile

30S ribosomal protein S12

Accession: KP13_31772

Gene: AHE42357.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GU37
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Length 124
Pocket druggability (P2Rank · AlphaFold DB model) 0.023
Direct ligand evidence 0 65 total records
Functional annotation 0 EC 6 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 13 structural and 2 bioactivity records.

Risks to review

Human similarity Top human hit identity: 48.182%. Microbiome similarity 3951 of 4744 screened genomes (83.3%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.17. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.02.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
48.182 Lower values reduce human off-target concern.
Human E-value
1.22e-28
Gut microbiome similarity
83.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
99.194 Higher values support similarity to known essential genes.
DEG E-value
2.53e-88 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.57 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.023
Structure A0A0H3GU37
Pocket Pocket 1
Druggability (FPocket) 0.171
Structure A0A0H3GU37
Pocket Pocket 3
ColabFold model
P2Rank 0.074 · Pocket 1
FPocket 0.164 · Pocket 7
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3951 / 4744 genomes with a hit
Prevalence 83.3%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GU37

Chemistry

ChEMBL DWT ChEMBL DXH

Sequence

Primary amino-acid sequence viewer.

MATINQLVRKPRARKVAKSNVPALEACPQKRGVCTRVYTTTPKKPNSALRKVCRVRLTNGFEVTSYIGGEGHNLQEHSVILIRGGRVKDLPGVRYHTVRGALDCSGVKDRKQARSKYGVKRPKA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

6
  • 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:0019843 Binding to a ribosomal RNA.
  • GO:0000049 Binding to a transfer RNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
1 124 FunFam G3DSA:2.40.50.140:FF:000001 30S ribosomal protein S12
12 123 Pfam PF00164 Ribosomal protein S12/S23
12 123 InterPro IPR006032 Ribosomal protein S12/S23
3 110 CDD cd03368 Ribosomal_S12
3 110 InterPro IPR005679 Ribosomal protein S12, bacterial-type
1 124 Gene3D G3DSA:2.40.50.140 -
1 124 InterPro IPR012340 Nucleic acid-binding, OB-fold
18 123 PANTHER PTHR11652 30S RIBOSOMAL PROTEIN S12 FAMILY MEMBER
18 123 InterPro IPR006032 Ribosomal protein S12/S23
1 124 PIRSF PIRSF002133 RPS12p_RPS12a_RPS23e_RPS12o
1 124 InterPro IPR006032 Ribosomal protein S12/S23
3 123 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
3 123 InterPro IPR012340 Nucleic acid-binding, OB-fold
110 122 PRINTS PR01034 Ribosomal protein S12 signature
110 122 InterPro IPR006032 Ribosomal protein S12/S23
94 110 PRINTS PR01034 Ribosomal protein S12 signature
94 110 InterPro IPR006032 Ribosomal protein S12/S23
58 77 PRINTS PR01034 Ribosomal protein S12 signature
58 77 InterPro IPR006032 Ribosomal protein S12/S23
27 42 PRINTS PR01034 Ribosomal protein S12 signature
27 42 InterPro IPR006032 Ribosomal protein S12/S23
77 94 PRINTS PR01034 Ribosomal protein S12 signature
77 94 InterPro IPR006032 Ribosomal protein S12/S23
42 57 PRINTS PR01034 Ribosomal protein S12 signature
42 57 InterPro IPR006032 Ribosomal protein S12/S23
1 123 Hamap MF_00403_B 30S ribosomal protein S12 [rpsL].
1 123 InterPro IPR005679 Ribosomal protein S12, bacterial-type
43 50 ProSitePatterns PS00055 Ribosomal protein S12 signature.
43 50 InterPro IPR006032 Ribosomal protein S12/S23
1 124 NCBIfam TIGR00981 30S ribosomal protein S12
1 124 InterPro IPR005679 Ribosomal protein S12, bacterial-type

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.023
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GU37
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_31772
ColabFold — — full sequence — Loaded

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.

65 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 15 records from similar proteins
Structural ligands 13 0 loaded crystals
Measured bioactivity 2 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3TS PDB via homolog 740.2 Da · LogP -5.98 · TPSA 336.3 Open detail RCSB PDB
AM2 PDB via homolog Detail RCSB PDB
FES PDB via homolog Detail RCSB PDB
GCP PDB via homolog Detail RCSB PDB
GNP PDB via homolog Detail RCSB PDB

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
3TS RCSB PDB
4B3T
Q5SHN3 740.2 Da LogP -5.98 TPSA 336.3 3 viol. ✓ Clean c1cc(ccc1CO[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O)…
AM2 RCSB PDB
4AQY
Q5SHN3 539.6 Da LogP -6.95 TPSA 283.6 3 viol. ✓ Clean CN[C@H]1[C@H]([C@@H]2[C@H](C[C@H]([C@H](O2)O[C@…
FES RCSB PDB
6RW4
O15235 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
GCP RCSB PDB
4V8Y
P0CX29 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…
GNP RCSB PDB
6RW5
O15235 522.2 Da LogP -2.76 TPSA 301.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
LLL RCSB PDB
5OBM
P0CX29 449.5 Da LogP -3.98 TPSA 213.7 2 viol. ✓ Clean C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H…
M5Z RCSB PDB
4B3R
Q5SHN3 731.8 Da LogP -5.84 TPSA 325.3 3 viol. ✓ Clean c1ccc(cc1)CC[C@@H]2OC[C@@H]3[C@@H](O2)[C@@H]([C…
OHX RCSB PDB
4V8E
Q5SHN3 286.4 Da LogP -3.55 TPSA 156.1 1 viol. ✓ Clean N[Os](N)(N)(N)(N)N
ON0 RCSB PDB
4B3M
Q5SHN3 703.7 Da LogP -6.10 TPSA 325.3 3 viol. ✓ Clean c1ccc(cc1)[C@@H]2OC[C@@H]3[C@@H](O2)[C@@H]([C@H…
PAR RCSB PDB
4LF7
F6DEQ7 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@…
RPO RCSB PDB
4B3S
Q5SHN3 705.8 Da LogP -6.64 TPSA 336.3 3 viol. ✓ Clean c1ccc(cc1)CO[C@@H]2[C@H](O[C@@H]([C@@H]([C@H]2O…
SCM RCSB PDB
1FJG
Q5SHN3 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 RCSB PDB
6RW4
O15235 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]([…

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.