Protein profile

VK055_0016

cytosine-specific methyltransferase

Genome: KpATCC43816

Gene: dcm AIK78647.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GV12
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Amino acids 464
Annotations 7
Features 26
PDB binders 3
Druggability 0.205

Overview

Basic information about this protein and its source genome.

Accession
VK055_0016
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
dcm AIK78647.1
Status
annotated
Amino acids
464
Structure source
AlphaFold + ColabFold
EC
2.1.1.37
GO
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0003886 Catalysis of the reaction: a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl-2'-deoxycytidine in DNA + H+ + S-adenosyl-L-homocysteine. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid). 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:0032259 The process in which a methyl group is covalently attached to a molecule. GO:0044027 An epigenetic gene regulation mechanism that negatively regulates gene expression by methylation of cytosine residues in chromosomal CpG islands. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide associated with the transcription start site of genes.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
25.967
Human E-value
1.71e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
78.043
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
92.28

Selected Druggability evidence

AlphaFold / UniProt model

Selected 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.

FPocket 0.205
Structure A0A0H3GV12
Pocket Pocket 22
P2Rank 0.578
Structure A0A0H3GV12
Pocket Pocket 1
ColabFold model
FPocket 0.605 · Pocket 6
P2Rank 0.613 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 107 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

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:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • GO:0003886 Catalysis of the reaction: a 2'-deoxycytidine in DNA + S-adenosyl-L-methionine = a 5-methyl-2'-deoxycytidine in DNA + H+ + S-adenosyl-L-homocysteine.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • 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:0032259 The process in which a methyl group is covalently attached to a molecule.
  • GO:0044027 An epigenetic gene regulation mechanism that negatively regulates gene expression by methylation of cytosine residues in chromosomal CpG islands. CpG islands are genomic regions that contain a high frequency of the CG dinucleotide associated with the transcription start site of genes.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
7 75 Gene3D G3DSA:1.10.260.140 -
424 442 ProSitePatterns PS00095 C-5 cytosine-specific DNA methylases C-terminal signature.
424 442 InterPro IPR031303 DNA methylase, C-5 cytosine-specific, conserved site
79 443 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
79 443 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
297 411 Gene3D G3DSA:3.90.120.30 -
263 276 PRINTS PR00105 Cytosine-specific DNA methyltransferase signature
263 276 InterPro IPR001525 C-5 cytosine methyltransferase
80 96 PRINTS PR00105 Cytosine-specific DNA methyltransferase signature
80 96 InterPro IPR001525 C-5 cytosine methyltransferase
209 223 PRINTS PR00105 Cytosine-specific DNA methyltransferase signature
209 223 InterPro IPR001525 C-5 cytosine methyltransferase
11 67 Pfam PF18284 DNA methylase N-terminal domain
11 67 InterPro IPR040743 DNA methylase N-terminal domain
79 429 CDD cd00315 Cyt_C5_DNA_methylase
380 454 PANTHER PTHR10629 CYTOSINE-SPECIFIC METHYLTRANSFERASE
79 440 Pfam PF00145 C-5 cytosine-specific DNA methylase
79 440 InterPro IPR001525 C-5 cytosine methyltransferase
79 449 ProSiteProfiles PS51679 C-5 cytosine-specific DNA methylase (Dnmt) domain profile.
79 449 InterPro IPR001525 C-5 cytosine methyltransferase
81 442 NCBIfam TIGR00675 DNA (cytosine-5-)-methyltransferase
81 442 InterPro IPR001525 C-5 cytosine methyltransferase
161 173 ProSitePatterns PS00094 C-5 cytosine-specific DNA methylases active site.
161 173 InterPro IPR018117 DNA methylase, C-5 cytosine-specific, active site
76 295 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
76 295 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; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GV12
AlphaFold — — full sequence — Viewing
ColabFold VK055_0016
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
22 0.205

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 5.47 0.26
2 2.34 0.061
3 2.03 0.044
4 1.57 0.024
5 1.38 0.017

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.

67 records

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
DCZ
2Z6Q
P05102 227.2 Da LogP -1.53 TPSA 110.6 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO)O
SFG
3SWR
P26358 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)…
X52
6X9J
P26358 472.6 Da LogP 2.73 TPSA 113.1 ✓ Ro5 ✓ Clean CCc1c(c(nc(c1C#N)SCc2ccc(cc2)N(C)S(=O)(=O)C)N(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.