KpKP13 Protein target profile

Ribosomal protein S12 methylthiotransferase RimO

Accession: KP13_04279

Gene: AHE45513.1 rimO 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GLY2

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Length 441

Pocket druggability (P2Rank · AlphaFold DB model) 0.913

Direct ligand evidence 0 15 total records

Functional annotation 0 EC 8 GO

Target summary

Promising target candidate with multiple supporting evidence streams.

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. Moderate predicted binding pocket FPocket selected-pocket score 0.50. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.91. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

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 (%): 31.677 Lower values reduce human off-target concern.
Human E-value: 2.28e-11
Gut microbiome similarity: 4.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 94.558 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 93.65 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) 0.913

Structure A0A0H3GLY2

Pocket Pocket 1

Druggability (FPocket) 0.499

Structure A0A0H3GLY2

Pocket Pocket 2

ColabFold model

P2Rank 0.924 · Pocket 1

FPocket 0.759 · Pocket 26

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 234 / 4744 genomes with a hit

Prevalence 4.9%

Sequence

Primary amino-acid sequence viewer.

MSNVTHQPKIGFVSLGCPKNLVDSERILTELRTEGYDVVPTYDNADMVIVNTCGFIDSAVQESLEAIGEALKENGKVIVTGCLGAKEDQIREVHPKVLEITGPHSYEQVLEHVHHYTPKPKHNPFLSLVPEQGVKLTPRHYAYLKISEGCNHRCTFCIIPSMRGDLVSRPIGEVLAEAKRLADAGVKELLVISQDTSAYGVDVKHRTGFHNGMPVKTSMVSLCEELAKLGIWVRLHYVYPYPHVDDVIPLMAEGKILPYLDIPLQHASPRILKLMKRPGSADRQLARIKQWREICPDLTLRSTFIVGFPGETEEDFQMLLDFLKEARLDRVGCFKYSPVEGATANELADQVPEEVKEERWNRFMQLQQQISAERLQEKVGREILVLVDEVDEEGAIGRSMADAPEIDGAVYLNGETRVKPGDVVRVKVEHADEYDLWGTRV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0035596 Catalysis of the addition of a methylthioether group (-SCH3) to a nucleic acid or protein acceptor.
GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
GO:0006400 The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
GO:0018339 The modification of peptidyl-aspartic acid to form peptidyl-L-beta-methylthioaspartic acid, typical of bacterial ribosomal protein S12.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

40 records

Show feature table

Start	End	DB	Term	Name
106	371	SUPERFAMILY	SSF102114	Radical SAM enzymes
53	362	SFLD	SFLDG01082	B12-binding domain containing
138	379	FunFam	G3DSA:3.80.30.20:FF:000001	tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase 2
146	323	Pfam	PF04055	Radical SAM superfamily
146	323	InterPro	IPR007197	Radical SAM
140	365	SMART	SM00729	MiaB
140	365	InterPro	IPR006638	Elp3/MiaA/NifB-like, radical SAM core domain
380	441	Gene3D	G3DSA:2.40.50.140	-
380	441	InterPro	IPR012340	Nucleic acid-binding, OB-fold
5	439	SFLD	SFLDF00274	ribosomal protein S12 methylthiotransferase (RimO-like)
5	439	InterPro	IPR005840	Ribosomal protein S12 methylthiotransferase RimO
9	438	NCBIfam	TIGR01125	30S ribosomal protein S12 methylthiotransferase RimO
9	438	InterPro	IPR005840	Ribosomal protein S12 methylthiotransferase RimO
5	440	PANTHER	PTHR43837	RIBOSOMAL PROTEIN S12 METHYLTHIOTRANSFERASE RIMO
5	440	InterPro	IPR005840	Ribosomal protein S12 methylthiotransferase RimO
379	441	Pfam	PF18693	TRAM domain
379	441	InterPro	IPR041582	RimO, TRAM domain
136	373	ProSiteProfiles	PS51918	Radical SAM core domain profile.
136	373	InterPro	IPR007197	Radical SAM
5	439	SFLD	SFLDG01061	methylthiotransferase
5	439	InterPro	IPR005839	Methylthiotransferase
138	379	Gene3D	G3DSA:3.80.30.20	tm_1862 like domain
138	379	InterPro	IPR023404	Radical SAM, alpha/beta horseshoe
9	125	FunFam	G3DSA:3.40.50.12160:FF:000002	Ribosomal protein S12 methylthiotransferase RimO
144	164	ProSitePatterns	PS01278	Methylthiotransferase radical SAM domain signature.
144	164	InterPro	IPR020612	Methylthiotransferase, conserved site
8	118	ProSiteProfiles	PS51449	Methylthiotransferase N-terminal domain profile.
8	118	InterPro	IPR013848	Methylthiotransferase, N-terminal
9	438	NCBIfam	TIGR00089	MiaB/RimO family radical SAM methylthiotransferase
9	438	InterPro	IPR005839	Methylthiotransferase
9	95	Pfam	PF00919	Uncharacterized protein family UPF0004
9	95	InterPro	IPR013848	Methylthiotransferase, N-terminal
9	126	Gene3D	G3DSA:3.40.50.12160	-
9	126	InterPro	IPR038135	Methylthiotransferase, N-terminal domain superfamily
376	441	ProSiteProfiles	PS50926	TRAM domain profile.
376	441	InterPro	IPR002792	TRAM domain
144	354	CDD	cd01335	Radical_SAM
8	440	Hamap	MF_01865	Ribosomal protein S12 methylthiotransferase RimO [rimO].
8	440	InterPro	IPR005840	Ribosomal protein S12 methylthiotransferase RimO
380	441	FunFam	G3DSA:2.40.50.140:FF:000060	Ribosomal protein S12 methylthiotransferase RimO

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.

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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

0.913

Likely same site as FPocket 27 6.7 Å 13 shared residues 93% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.347

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Surrounding area

Pocket 3 P2Rank #3

0.294

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Surrounding area

Pocket 4 P2Rank #4

0.06

Likely same site as FPocket 2 2.8 Å 8 shared residues 100% of smaller site

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Surrounding area

Pocket 5 P2Rank #5

0.007

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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #2

0.499

Likely same site as P2Rank 4 2.8 Å 8 shared residues 100% of smaller site

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Surrounding area

Pocket 2 FPocket #27

0.363

Likely same site as P2Rank 1 6.7 Å 13 shared residues 93% of smaller site

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Surrounding area

Residue sets

UniProt: Binding site:150-150

UniProt: Binding site:154-154

UniProt: Binding site:157-157

UniProt: Binding site:17-17

UniProt: Binding site:53-53

UniProt: Binding site:82-82

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.924

Likely same site as FPocket 32 3.1 Å 19 shared residues 95% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.326

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Surrounding area

Pocket 3 P2Rank #3

0.097

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Surrounding area

Pocket 4 P2Rank #4

0.044

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Surrounding area

Pocket 5 P2Rank #5

0.04

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Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #26

0.759

Likely same site as P2Rank 1 5.9 Å 11 shared residues 85% of smaller site

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Surrounding area

Pocket 2 FPocket #32

0.615

Likely same site as P2Rank 1 3.1 Å 19 shared residues 95% of smaller site

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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_A0A0H3GLY2	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_04279	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.

15 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 2 records from similar proteins

Structural ligands 2 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 13 similarity-based ZINC candidates

Best available ligand signal

CXS PDB via homolog 221.3 Da · LogP 1.19 · TPSA 66.4 Open detail RCSB PDB

FS5 PDB via homolog Detail RCSB PDB

ZINC2004372 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC38364153 ZINC proposed compound · Tanimoto 0.926 Detail ZINC

ZINC1710230 ZINC proposed compound · Tanimoto 0.786 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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
CXS RCSB PDB	2QGQ	Q9X2H6	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`C1CCC(CC1)NCCCS(=O)(=O)O`
FS5 RCSB PDB	4JC0	Q9X2H6	863.6 Da LogP 8.41 TPSA 0.0	2 viol.	✓ Clean	`S(SS[Fe]12[S]3[Fe]4[S]1[Fe]5[S]4[Fe]3[S]25)SS[F…`

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
ZINC2004372 ZINC	1.000	221.3 Da LogP 1.19 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCNC1CCCCC1`
ZINC38364153 ZINC	0.926	235.3 Da LogP 1.58 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCCCNC1CCCCC1`
ZINC1710230 ZINC	0.786	207.3 Da LogP 0.80 TPSA 66.4	✓ Ro5	✓ Clean	`O=S(=O)(O)CCNC1CCCCC1`
ZINC5188799 ZINC	0.630	280.5 Da LogP 4.39 TPSA 24.1	✓ Ro5	✓ Clean	`C(CCCNC1CCCCC1)CCNC1CCCCC1`
ZINC2509149 ZINC	0.531	211.4 Da LogP 4.27 TPSA 12.0	✓ Ro5	✓ Clean	`CCCCCCCCNC1CCCCC1`
ZINC130127586 ZINC	0.529	260.4 Da LogP 1.38 TPSA 58.2	✓ Ro5	✓ Clean	`O=S(=O)(NCCNC1CCCCCC1)C1CC1`
ZINC19367005 ZINC	0.519	224.4 Da LogP 2.83 TPSA 24.1	✓ Ro5	✓ Clean	`C1CCC(NCCNC2CCCCC2)CC1`
ZINC1672446 ZINC	0.500	228.3 Da LogP 1.49 TPSA 75.3	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC1CCCCC1)C(=O)O`
ZINC2168583 ZINC	0.500	237.3 Da LogP 0.16 TPSA 86.6	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@@H](O)CNC1CCCCC1`
ZINC2168584 ZINC	0.500	237.3 Da LogP 0.16 TPSA 86.6	✓ Ro5	✓ Clean	`O=S(=O)(O)C[C@H](O)CNC1CCCCC1`
ZINC236994621 ZINC	0.500	290.4 Da LogP 0.85 TPSA 75.3	✓ Ro5	✓ Clean	`CCS(=O)(=O)CC(=O)NCCNC1CCCCCC1`
ZINC44655186 ZINC	0.500	213.4 Da LogP 3.12 TPSA 21.3	✓ Ro5	✓ Clean	`COCCCCNC1CCCCCCC1`
ZINC5840523 ZINC	0.500	228.3 Da LogP 1.49 TPSA 75.3	✓ Ro5	✓ Clean	`N[C@H](CCCCNC1CCCCC1)C(=O)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.

Cross-references

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

Sequence

UniProt A0A0H3GLY2