KpATCC43816 Protein target profile

16S rRNA m2G1207 methyltransferase

Accession: VK055_2604

Gene: AIK81201.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GIT7
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Length 342
Pocket druggability (P2Rank · AlphaFold DB model) 0.867
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 55 total records
Functional annotation 1 EC 9 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

No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.87. Review the complete evidence below

Risks to review

Microbiome similarity 107 of 4744 screened genomes (2.3%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.87) — check the ligand evidence before deprioritizing on off-target risk alone. Weak predicted binding pocket FPocket selected-pocket score 0.39.

Evidence coverage

Core evidence streams are available for this target.
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
No hit
Gut microbiome similarity
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
36.634 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
94.51 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) 0.867
Structure A0A0H3GIT7
Pocket Pocket 1
Druggability (FPocket) 0.394
Structure A0A0H3GIT7
Pocket Pocket 4
ColabFold model
P2Rank 0.84 · Pocket 1
FPocket 0.146 · Pocket 19
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 107 / 4744 genomes with a hit
Prevalence 2.3%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSAFTPASEVLLRHSDDFESARVLFAGDLQDDLPARLDTAASRAHTQQFHHWQVLNRQMGDTVRFSLVAEAADVAECDTLIYYWPKNKPEAQFQLMNLLSLLPVGSDIFVVGENRSGVRSAEQMLAEYAPLNKVDSARRCGLYHGRLEKQPTFDADAFWGEYTLDNLTIKTLPGVFSRDGLDVGSQLLLSTLEPHTKGKVLDVGCGAGVLAAALASHSPKVRLTLCDVSAPAVEASRATLAANGLAGDVFASNVFSEVNGRFDMIISNPPFHDGLQTSLEAAQALIRGAVRHLNSGGELRIVANAFLPYPQVLDETFGFHEVIAQTGRFKVYRTIMTRQAKK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0008757 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
  • GO:0008649 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule. The methyl group can be transfered to the nucleobase or to the ribose group of the nucleoside.
  • GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
  • GO:0003676 Binding to a nucleic acid.
  • GO:0008990 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine.
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0052914 Catalysis of the reaction: S-adenosyl-L-methionine + guanosine(1207) in 16S rRNA = N(2)-methylguanosine(1207) in 16S rRNA + S-adenosyl-L-homocysteine.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
1 158 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
1 158 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
199 299 CDD cd02440 AdoMet_MTases
159 342 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
159 342 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
167 333 Pfam PF05175 Methyltransferase small domain
167 333 InterPro IPR007848 Methyltransferase small domain
265 271 ProSitePatterns PS00092 N-6 Adenine-specific DNA methylases signature.
265 271 InterPro IPR002052 DNA methylase, N-6 adenine-specific, conserved site
4 336 PANTHER PTHR47816 RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE C
4 336 InterPro IPR046977 rRNA (guanine-N(2)-)-methyltransferase RsmC/RlmG
107 325 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
107 325 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
4 336 Hamap MF_01862 Ribosomal RNA small subunit methyltransferase C [rsmC].
4 336 InterPro IPR023543 rRNA small subunit methyltransferase C
8 162 Pfam PF08468 Methyltransferase small domain N-terminal
8 162 InterPro IPR013675 Methyltransferase small, N-terminal

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
0.867
Likely same site as FPocket 4 1.1 Å 26 shared residues 90% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.208
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Surrounding area
Pocket 3 P2Rank #3
0.08
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Surrounding area
Pocket 4 P2Rank #4
0.005
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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 #4
0.394 Unusual size
Likely same site as P2Rank 1 1.1 Å 26 shared residues 90% 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_A0A0H3GIT7
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2604
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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
7QM PDB via homolog 497.5 Da · LogP -7.06 · TPSA 274.4 Open detail RCSB PDB
7XP PDB via homolog Detail RCSB PDB
827 PDB via homolog Detail RCSB PDB
9CS PDB via homolog Detail RCSB PDB
GET 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
7QM RCSB PDB
5U1I
Q2MG72 497.5 Da LogP -7.06 TPSA 274.4 2 viol. ✓ Clean CN[C@H]1[C@@H]([C@H](O[C@@H]([C@@H]1O)O[C@H]2[C…
7XP RCSB PDB
5U0N
Q2MG72 454.5 Da LogP -6.65 TPSA 262.4 2 viol. ✓ Clean C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C…
827 RCSB PDB
5U19
Q2MG72 482.5 Da LogP -6.00 TPSA 248.4 2 viol. ✓ Clean C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H…
9CS RCSB PDB
5U1E
Q2MG72 483.5 Da LogP -7.33 TPSA 288.4 2 viol. ✓ Clean C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C…
GET RCSB PDB
5U18
Q2MG72 496.6 Da LogP -5.61 TPSA 248.4 2 viol. ✓ Clean C[C@H]([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[C@@…

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 A0A0H3GIT7

Pathways

BioCyc RXN-11576