Protein target profile

KP13_05032

Methylated-DNA--protein-cysteine methyltransferase

Genome: KpKP13 Gene: AHE44793.1 ogt 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSX7
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Length 175
Pocket druggability 0.069
Direct ligand evidence 0 53 total records
Functional annotation 1 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 3 structural and 0 bioactivity records.

Risks to review

Human similarity Top human hit identity: 45.536%. Microbiome similarity 79 of 4744 screened genomes (1.7%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.07. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.10.

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 (%)
45.536 Lower values reduce human off-target concern.
Human E-value
2.5000000000000002e-21
Gut microbiome similarity
1.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
43.312 Higher values support similarity to known essential genes.
DEG E-value
2.8200000000000002e-33 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
94.53 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 0.069
Structure A0A0H3GSX7
Pocket Pocket 9
P2Rank 0.1
Structure A0A0H3GSX7
Pocket Pocket 1
ColabFold model
FPocket 0.094 · Pocket 9
P2Rank 0.032 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 79 / 4744 genomes with a hit
Prevalence 1.7%

Cross-references

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

Sequence

UniProt A0A0H3GSX7

Sequence

Primary amino-acid sequence viewer.

MTETMLTLLQDKMDTPLGPLWVLCDEQFNLRAVEWDEHRDRMETLLDVHYRREGYQRVDCRNPGGLSSKLSDYFAGDLAIIETLPTATAGTPFQRQVWQALRDIPCGQVMHYGQLAEALGRPGAARAVGAANGANPVSIVVPCHRVIGRNGTMTGYAGGVQRKEWLLRHEGYLLL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0003908 Catalysis of the reaction: DNA (containing 6-O-methylguanine) + (protein)-L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine.
  • 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:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0006307 The repair of alkylation damage in DNA, e.g. the removal of a non-physiological alkyl group from a nucleobase. This is usually mediated by DNA alkyltransferases.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
141 147 ProSitePatterns PS00374 Methylated-DNA--protein-cysteine methyltransferase active site.
141 147 InterPro IPR001497 Methylated-DNA-[protein]-cysteine S-methyltransferase, active site
93 171 CDD cd06445 ATase
93 171 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
12 171 Hamap MF_00772 Methylated-DNA--protein-cysteine methyltransferase [ogt].
12 171 InterPro IPR023546 Methylated-DNA--protein-cysteine methyltransferase
8 172 PANTHER PTHR10815 METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE
90 173 SUPERFAMILY SSF46767 Methylated DNA-protein cysteine methyltransferase, C-terminal domain
90 173 InterPro IPR036217 Methylated DNA-protein cysteine methyltransferase, DNA binding domain
11 96 SUPERFAMILY SSF53155 Methylated DNA-protein cysteine methyltransferase domain
11 96 InterPro IPR036631 Methylated DNA-protein cysteine methyltransferase domain superfamily
88 171 Gene3D G3DSA:1.10.10.10 -
88 171 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
89 172 FunFam G3DSA:1.10.10.10:FF:000337 Methylated-DNA--protein-cysteine methyltransferase
92 171 Pfam PF01035 6-O-methylguanine DNA methyltransferase, DNA binding domain
92 171 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
91 170 NCBIfam TIGR00589 methylated-DNA--[protein]-cysteine S-methyltransferase
91 170 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
8 87 Pfam PF02870 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain
8 87 InterPro IPR008332 Methylguanine DNA methyltransferase, ribonuclease-like domain

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

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

Site 1 P2Rank #1
0.1
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.009
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:139-139 Nucleophile; methyl group acceptor
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_A0A0H3GSX7
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_05032
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

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ETW PDB via homolog 479.5 Da · LogP 5.21 · TPSA 116.8 Open detail RCSB PDB
OGQ PDB via homolog Detail RCSB PDB
PBO PDB via homolog Detail RCSB PDB
ZINC100071118 ZINC proposed compound · Tanimoto 0.758 Detail ZINC
ZINC100071122 ZINC proposed compound · Tanimoto 0.758 Detail ZINC

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
ETW RCSB PDB
6GA0
Q97VW7 479.5 Da LogP 5.21 TPSA 116.8 1 viol. ✓ Clean Cc1ccc(cc1)CNC(=O)c2ccc(c(c2)C(=O)O)C3=C4C=CC(=…
OGQ RCSB PDB
6Y8P
E5BBQ0 534.6 Da LogP 5.24 TPSA 85.8 2 viol. ✓ Clean Cc1ccc(cc1)CNC(=O)c2ccc(c(c2)C3=C4C=CC(=[N+](C)…
PBO RCSB PDB
3GYH
Q9UTN9 149.2 Da LogP 2.06 TPSA 30.0 ✓ Ro5 ✓ Clean CCCC(=O)c1cccnc1

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.