Protein profile
KP13_00170
methylated-DNA/protein-cysteine methyltransferase
Genome: KpKP13
Overview
Basic information about this protein and its source genome.
- Accession
- KP13_00170
- Gene
- AHE42090.1
- Status
- annotated
- Amino acids
- 352
- Structure source
- AlphaFold + ColabFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 31.325
- Human E-value
- 2.39e-16
- Gut microbiome off-target
- hit
- Essential (DEG)
- N
- DEG identity (%)
- 0.0
- Localization
- Cytoplasmic
- ColabFold pLDDT
- 87.03
Selected Druggability evidence
AlphaFold / UniProt modelSelected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Enzyme Commission (EC)
1Gene Ontology (GO)
10- 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 Features
Domain/signature hits from InterPro and related databases.
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; predicted models typically cover the full protein.
Loading 3D structure...
Structural evidence
0 + 2Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
AF_A0A0H3H068
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_00170
|
ColabFold | — | — | full sequence | — | Loaded |
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer
Pockets (FPOCKET)
Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).
| FPOCKET | Sticks | Spheres | Surfaces | Druggability | Labels | Zoom | Positions |
|---|---|---|---|---|---|---|---|
| 3 | 0.843 |
Pockets (P2RANK)
Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).
| P2RANK | Sticks | Spheres | Surfaces | Score | Probability | Labels | Zoom | Positions |
|---|---|---|---|---|---|---|---|---|
| 1 | 4.65 | 0.202 | ||||||
| 2 | 3.85 | 0.15 | ||||||
| 3 | 3.13 | 0.105 | ||||||
| 4 | 2.96 | 0.096 | ||||||
| 5 | 2.9 | 0.093 |
Pockets (FPOCKET)
Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).
| FPOCKET | Sticks | Spheres | Surfaces | Druggability | Labels | Zoom | Positions |
|---|---|---|---|---|---|---|---|
| 25 | 0.623 | ||||||
| 2 | 0.465 |
Pockets (P2RANK)
Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).
| P2RANK | Sticks | Spheres | Surfaces | Score | Probability | Labels | Zoom | Positions |
|---|---|---|---|---|---|---|---|---|
| 1 | 3.2 | 0.11 | ||||||
| 2 | 2.49 | 0.069 | ||||||
| 3 | 2.32 | 0.059 | ||||||
| 4 | 1.46 | 0.02 | ||||||
| 5 | 1.19 | 0.01 |
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.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, 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.
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 | 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 | 0.529 | 346.3 Da LogP 4.06 TPSA 76.7 | ✓ Ro5 | ✓ Clean |
COC(=O)c1ccccc1-c1c2ccc(=O)cc-2oc2cc(O)ccc12
|
| ZINC5030626 | 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.