Protein profile

KP13_04837

DNA-cytosine methyltransferase

Genome: KpKP13

Gene: dcm AHE43805.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GV12
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Amino acids 481
Annotations 7
Features 26
PDB binders 3
Druggability 0.205

Overview

Basic information about this protein and its source genome.

Accession
KP13_04837
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
dcm AHE43805.1
Status
annotated
Amino acids
481
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
1.32e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
77.07
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
90.18

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 0.56 · Pocket 11
P2Rank 0.592 · 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
441 459 ProSitePatterns PS00095 C-5 cytosine-specific DNA methylases C-terminal signature.
441 459 InterPro IPR031303 DNA methylase, C-5 cytosine-specific, conserved site
314 428 Gene3D G3DSA:3.90.120.30 -
280 293 PRINTS PR00105 Cytosine-specific DNA methyltransferase signature
280 293 InterPro IPR001525 C-5 cytosine methyltransferase
97 113 PRINTS PR00105 Cytosine-specific DNA methyltransferase signature
97 113 InterPro IPR001525 C-5 cytosine methyltransferase
226 240 PRINTS PR00105 Cytosine-specific DNA methyltransferase signature
226 240 InterPro IPR001525 C-5 cytosine methyltransferase
98 459 NCBIfam TIGR00675 DNA (cytosine-5-)-methyltransferase
98 459 InterPro IPR001525 C-5 cytosine methyltransferase
96 460 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
96 460 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
93 312 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
93 312 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
28 84 Pfam PF18284 DNA methylase N-terminal domain
28 84 InterPro IPR040743 DNA methylase N-terminal domain
96 446 CDD cd00315 Cyt_C5_DNA_methylase
24 92 Gene3D G3DSA:1.10.260.140 -
96 457 Pfam PF00145 C-5 cytosine-specific DNA methylase
96 457 InterPro IPR001525 C-5 cytosine methyltransferase
178 190 ProSitePatterns PS00094 C-5 cytosine-specific DNA methylases active site.
178 190 InterPro IPR018117 DNA methylase, C-5 cytosine-specific, active site
397 471 PANTHER PTHR10629 CYTOSINE-SPECIFIC METHYLTRANSFERASE
96 466 ProSiteProfiles PS51679 C-5 cytosine-specific DNA methylase (Dnmt) domain profile.
96 466 InterPro IPR001525 C-5 cytosine methyltransferase

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 KP13_04837
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.