Protein target profile

VK055_5159

DNA adenine methylase family protein

Genome: KpATCC43816 Gene: AIK83680.1 dam2 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A9Q8FFK7
Length 269
Pocket druggability 0.932
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 53 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.

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
0.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
42.963 Higher values support similarity to known essential genes.
DEG E-value
7.46e-70 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Unknown

Structure confidence

ColabFold pLDDT
89.56 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.932
Structure A0A9Q8FFK7
Pocket Pocket 1
P2Rank 0.846
Structure A0A9Q8FFK7
Pocket Pocket 1
ColabFold model
FPocket 0.855 · Pocket 1
P2Rank 0.868 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 6 / 4744 genomes with a hit
Prevalence 0.1%

Cross-references

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

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.

MSKPFLKWAGGKYTQLADLFVHIPAGKRLIEPFVGGGSVFLNSEKHADYLLADVNPDLINLYQMLAVVPDEVELKARWMFEHMRSPDGYELIRSEFNAQTLDATERAAAFLYLNRHCFNGLMRYNQANKFNVGWGGYKAPYYPMDEMKAFAAMAHHCVFMTADYRRTISLAGKGDVVYCDPPYETMPGTTGFTAYAAGGFSWDNQVDLAKQCVSAFHRGARVVISNSSAPKVLNLYREHGFNLQFINARRSISCKSSTREVAKDVVAIL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0003676 Binding to a nucleic acid.
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • GO:0009007 Catalysis of the reaction: S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine + DNA 6-methylaminopurine.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.
  • GO:0032775 OBSOLETE. The covalent transfer of a methyl group to N-6 of adenine in a DNA molecule.
  • GO:1904047 Binding to S-adenosyl-L-methionine.
  • GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
  • GO:0009307 A defense process found in many bacteria and archaea that protects the organism from invading foreign DNA by cleaving it with a restriction endonuclease. The organism's own DNA is protected by methylation of a specific nucleotide, which occurs immediately following replication, in the same target site as the restriction enzyme.
  • GO:0006298 A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
56 155 Gene3D G3DSA:1.10.1020.10 -
56 155 InterPro IPR023095 Adenine-specific methyltransferase, domain 2
3 267 NCBIfam TIGR00571 Dam family site-specific DNA-(adenine-N6)-methyltransferase
3 267 InterPro IPR012327 D12 class N6 adenine-specific DNA methyltransferase
1 267 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
1 267 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
177 183 ProSitePatterns PS00092 N-6 Adenine-specific DNA methylases signature.
177 183 InterPro IPR002052 DNA methylase, N-6 adenine-specific, conserved site
174 186 PRINTS PR00505 D12 class N6 adenine-specific DNA methyltransferase signature
174 186 InterPro IPR012327 D12 class N6 adenine-specific DNA methyltransferase
8 24 PRINTS PR00505 D12 class N6 adenine-specific DNA methyltransferase signature
8 24 InterPro IPR012327 D12 class N6 adenine-specific DNA methyltransferase
49 62 PRINTS PR00505 D12 class N6 adenine-specific DNA methyltransferase signature
49 62 InterPro IPR012327 D12 class N6 adenine-specific DNA methyltransferase
29 43 PRINTS PR00505 D12 class N6 adenine-specific DNA methyltransferase signature
29 43 InterPro IPR012327 D12 class N6 adenine-specific DNA methyltransferase
1 269 PIRSF PIRSF000398 M_m6A_EcoRV
1 269 InterPro IPR012263 Adenine modification methylase, M.EcoRV-type
2 267 PANTHER PTHR30481 DNA ADENINE METHYLASE
2 267 InterPro IPR012327 D12 class N6 adenine-specific DNA methyltransferase
8 250 Pfam PF02086 D12 class N6 adenine-specific DNA methyltransferase
8 250 InterPro IPR012327 D12 class N6 adenine-specific DNA methyltransferase
4 238 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
4 238 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily

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 · FPocket

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

Site 1 FPocket #1
0.932
Likely same site as P2Rank 1 4.7 Å 34 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.846
Likely same site as FPocket 1 4.7 Å 34 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.025
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_A0A9Q8FFK7
AlphaFold DB full sequence Viewing
ColabFold VK055_5159
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.

53 records
Chemistry signal

Bioactivity evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 0 0 loaded crystals
Measured bioactivity 3 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CHEMBL250656 ChEMBL via homolog 353.4 Da · LogP 0.45 · TPSA 130.8 Open detail ChEMBL
CHEMBL399890 ChEMBL via homolog Detail ChEMBL
SFG ChEMBL via homolog Detail ChEMBL
ZINC13650200 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC205994753 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

Show only:
Ligand UniProt (homolog) pchembl MW · LogP · TPSA Lipinski PAINS SMILES
CHEMBL250656 ChEMBL P0AEE8 353.4 Da LogP 0.45 TPSA 130.8 ✓ Ro5 ✓ Clean Nc1cccc2c1ncn2[C@@H]1O[C@H](CSCCC(=O)O)[C@@H](O…
CHEMBL399890 ChEMBL P0AEE8 355.4 Da LogP -0.76 TPSA 156.6 ✓ Ro5 ✓ Clean Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCCC(=O)O)[C@@H](O…
SFG ChEMBL P0AEE8 381.4 Da LogP -2.06 TPSA 208.7 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.