KpKP13 Protein target profile

methylated-DNA/protein-cysteine methyltransferase

Accession: KP13_00170

Gene: AHE42090.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H068

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Length 352

Pocket druggability (P2Rank · AlphaFold DB model) 0.419

Direct ligand evidence 0 5 total records

Functional annotation 1 EC 10 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. Strong predicted binding pocket FPocket selected-pocket score 0.84. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 2 structural and 0 bioactivity records.

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 (%): 31.325 Lower values reduce human off-target concern.
Human E-value: 2.39e-16
Gut microbiome similarity: 0.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 87.03 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) 0.419

Structure A0A0H3H068

Pocket Pocket 1

Druggability (FPocket) 0.843

Structure A0A0H3H068

Pocket Pocket 3

ColabFold model

P2Rank 0.129 · Pocket 1

FPocket 0.623 · Pocket 25

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 20 / 4744 genomes with a hit

Prevalence 0.4%

Sequence

Primary amino-acid sequence viewer.

MKITDSMQCDIWYQALLERAVEFTGVFFVGVKTTGVFCISVCRARKPRRENVEFYNDFKSALDAGFRPCKVCRPTENARTAPAFVEQALRLLREAPKVRLSDSELRQHDISPERVRRWFLQNHGITFQAFQRMQRLNMALQELKAGRSTTDVAFDSGYESLSGFGYTCKKLTGFAPSAQRQVVLIHRFTTPLGPMFVCATQRGICLLEFVDRRALESEFSDLQRRLNASIIAGENAHTRQAQQEITEYFAGQRQSFEVALDTPGSEFQRAVWRRLQHVSFGETTHYQSIAMEIGKPTATRAVAAANGANRVAIIIPCHRIIGKDGSMTGYGGGIARKIWLINHEATIREKRG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

2.1.1.63

Gene Ontology (GO)

GO:0008270 Binding to a zinc ion (Zn).
GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
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: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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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.

36 records

Show feature table

Start	End	DB	Term	Name
83	182	Gene3D	G3DSA:1.10.10.60	-
99	180	SMART	SM00342	aracneu4
99	180	InterPro	IPR018060	DNA binding HTH domain, AraC-type
186	349	PANTHER	PTHR10815	METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE
189	260	Pfam	PF02870	6-O-methylguanine DNA methyltransferase, ribonuclease-like domain
189	260	InterPro	IPR008332	Methylguanine DNA methyltransferase, ribonuclease-like domain
135	182	SUPERFAMILY	SSF46689	Homeodomain-like
135	182	InterPro	IPR009057	Homeobox-like domain superfamily
1	351	PIRSF	PIRSF000409	Ada
1	351	InterPro	IPR016221	Bifunctional regulatory protein Ada
264	345	SUPERFAMILY	SSF46767	Methylated DNA-protein cysteine methyltransferase, C-terminal domain
264	345	InterPro	IPR036217	Methylated DNA-protein cysteine methyltransferase, DNA binding domain
10	78	Gene3D	G3DSA:3.40.10.10	DNA Methylphosphotriester Repair Domain
10	78	InterPro	IPR035451	Ada-like domain superfamily
109	180	Pfam	PF12833	Helix-turn-helix domain
109	180	InterPro	IPR018060	DNA binding HTH domain, AraC-type
263	346	Gene3D	G3DSA:1.10.10.10	-
263	346	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
13	74	Pfam	PF02805	Metal binding domain of Ada
13	74	InterPro	IPR004026	Ada DNA repair, metal-binding
315	321	ProSitePatterns	PS00374	Methylated-DNA--protein-cysteine methyltransferase active site.
315	321	InterPro	IPR001497	Methylated-DNA-[protein]-cysteine S-methyltransferase, active site
110	182	ProSiteProfiles	PS01124	Bacterial regulatory proteins, araC family DNA-binding domain profile.
110	182	InterPro	IPR018060	DNA binding HTH domain, AraC-type
267	344	CDD	cd06445	ATase
267	344	InterPro	IPR014048	Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
266	345	Pfam	PF01035	6-O-methylguanine DNA methyltransferase, DNA binding domain
266	345	InterPro	IPR014048	Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
262	347	FunFam	G3DSA:1.10.10.10:FF:000214	Methylated-DNA--protein-cysteine methyltransferase
183	261	Gene3D	G3DSA:3.30.160.70	-
266	344	NCBIfam	TIGR00589	methylated-DNA--[protein]-cysteine S-methyltransferase
266	344	InterPro	IPR014048	Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
1	88	SUPERFAMILY	SSF57884	Ada DNA repair protein, N-terminal domain (N-Ada 10)
1	88	InterPro	IPR035451	Ada-like domain superfamily
185	261	SUPERFAMILY	SSF53155	Methylated DNA-protein cysteine methyltransferase domain
185	261	InterPro	IPR036631	Methylated DNA-protein cysteine methyltransferase domain 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 · P2Rank

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

Pocket 1 P2Rank #1

0.419

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Surrounding area

Pocket 2 P2Rank #2

0.235

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Surrounding area

Pocket 3 P2Rank #3

0.191

Likely same site as FPocket 3 2.8 Å 11 shared residues 100% of smaller site

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Surrounding area

Pocket 4 P2Rank #4

0.173

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Surrounding area

Pocket 5 P2Rank #5

0.085

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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 #3

0.843

Likely same site as P2Rank 3 2.8 Å 11 shared residues 100% of smaller site

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Surrounding area

Residue sets

UniProt: Active site:317-317 Nucleophile; methyl group acceptor from either O6-methylguanine or O4-methylthymine

UniProt: Active site:38-38 Nucleophile; methyl group acceptor from methylphosphotriester

UniProt: Binding site:34-34

UniProt: Binding site:38-38

UniProt: Binding site:42-42

UniProt: Binding site:43-43

UniProt: Binding site:45-45

UniProt: Binding site:67-67

UniProt: Binding site:69-69

UniProt: Binding site:72-72

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.129

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Surrounding area

Pocket 2 P2Rank #2

0.122

Likely same site as FPocket 25 2.2 Å 12 shared residues 92% of smaller site

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Surrounding area

Pocket 3 P2Rank #3

0.116

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Surrounding area

Pocket 4 P2Rank #4

0.116

Likely same site as FPocket 3 1.3 Å 8 shared residues 100% of smaller site

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Surrounding area

Pocket 5 P2Rank #5

0.033

Likely same site as FPocket 2 6.2 Å 11 shared residues 100% of smaller site

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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 #25

0.623 Unusual size

Likely same site as P2Rank 2 2.2 Å 12 shared residues 92% of smaller site

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Surrounding area

Pocket 2 FPocket #2

0.465 Unusual size

Likely same site as P2Rank 5 6.2 Å 11 shared residues 100% of smaller site

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Surrounding area

Pocket 3 FPocket #3

0.238

Likely same site as P2Rank 4 1.3 Å 8 shared residues 100% 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_A0A0H3H068	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_00170	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.

5 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 3 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

ZINC22054134 ZINC proposed compound · Tanimoto 0.723 Detail ZINC

ZINC4344388 ZINC proposed compound · Tanimoto 0.529 Detail ZINC

ZINC5030626 ZINC proposed compound · Tanimoto 0.500 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
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)…`

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
ZINC22054134 ZINC	0.723	431.5 Da LogP 3.70 TPSA 94.0	✓ Ro5	✓ Clean	`CN(C)c1ccc2c(-c3cc(C(=O)O)ccc3C(=O)O)c3ccc(=[N+…`
ZINC4344388 ZINC	0.529	346.3 Da LogP 4.06 TPSA 76.7	✓ Ro5	✓ Clean	`COC(=O)c1ccccc1-c1c2ccc(=O)cc-2oc2cc(O)ccc12`
ZINC5030626 ZINC	0.500	332.3 Da LogP 3.97 TPSA 87.7	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2c3ccc(=O)cc-3oc3cc(O)ccc23)c1`

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 A0A0H3H068