Protein profile

VK055_5150

C-5 cytosine-specific DNA methylase family protein

Genome: KpATCC43816

Gene: AIK83671.1 Structure source: ColabFold

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Amino acids 238

Annotations 1

Features 22

PDB binders 1

Druggability 0.187

Overview

Basic information about this protein and its source genome.

Accession: VK055_5150
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK83671.1
Status: annotated
Amino acids: 238
Structure source: ColabFold

GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 34.731
Localization: Unknown
ColabFold pLDDT: 80.88

Selected Druggability evidence

ColabFold / curated 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 0.187

Structure CB_VK055_5150

Pocket Pocket 24

P2Rank 0.311

Structure CB_VK055_5150

Pocket Pocket 1

ColabFold model

FPocket 0.187 · Pocket 24

P2Rank 0.311 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 1 / 4744 genomes with a hit

Normalized 0

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records

Show feature table

Start	End	DB	Term	Name
4	15	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	174	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
1	174	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
69	81	ProSitePatterns	PS00094	C-5 cytosine-specific DNA methylases active site.
69	81	InterPro	IPR018117	DNA methylase, C-5 cytosine-specific, active site
6	176	PANTHER	PTHR10629	CYTOSINE-SPECIFIC METHYLTRANSFERASE
1	27	Phobius	SIGNAL_PEPTIDE	Signal peptide region
16	27	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
2	18	PRINTS	PR00105	Cytosine-specific DNA methyltransferase signature
2	18	InterPro	IPR001525	C-5 cytosine methyltransferase
108	122	PRINTS	PR00105	Cytosine-specific DNA methyltransferase signature
108	122	InterPro	IPR001525	C-5 cytosine methyltransferase
150	163	PRINTS	PR00105	Cytosine-specific DNA methyltransferase signature
150	163	InterPro	IPR001525	C-5 cytosine methyltransferase
2	235	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
2	235	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
28	238	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	238	ProSiteProfiles	PS51679	C-5 cytosine-specific DNA methylase (Dnmt) domain profile.
1	238	InterPro	IPR001525	C-5 cytosine methyltransferase
4	164	Pfam	PF00145	C-5 cytosine-specific DNA methylase
4	164	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.

Loading 3D structure...

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Structural evidence

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
ColabFold VK055_5150	ColabFold	—	—	full sequence	—	Viewing

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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				3.14	0.106

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.

51 records

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.

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`

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
ZINC11612315	1.000	227.2 Da LogP -1.53 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)n1`
ZINC18286010	1.000	227.2 Da LogP -1.53 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@H](O)[C@@H](CO)O2)c(=O)n1`
ZINC18286013	1.000	227.2 Da LogP -1.53 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)n1`
ZINC3869837	1.000	227.2 Da LogP -1.53 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@H](O)[C@H](CO)O2)c(=O)n1`
ZINC3869838	1.000	227.2 Da LogP -1.53 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@@H](O)[C@H](CO)O2)c(=O)n1`
ZINC4253	1.000	227.2 Da LogP -1.53 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@@H](O)[C@H](CO)O2)c(=O)n1`
ZINC5239365	1.000	227.2 Da LogP -1.53 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)n1`
ZINC57290	1.000	227.2 Da LogP -1.53 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@H](O)[C@H](CO)O2)c(=O)n1`
ZINC34235488	0.810	226.2 Da LogP -1.57 TPSA 116.4	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2ccc(N)nc2=O)C[C@@H]1O`
ZINC2004224	0.791	226.2 Da LogP -1.57 TPSA 116.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@@H](N)[C@H](CO)O2)c(=O)n1`
ZINC5551931	0.791	226.2 Da LogP -1.57 TPSA 116.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@H](N)[C@H](CO)O2)c(=O)n1`
ZINC5551934	0.791	226.2 Da LogP -1.57 TPSA 116.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@H](N)[C@H](CO)O2)c(=O)n1`
ZINC5551938	0.791	226.2 Da LogP -1.57 TPSA 116.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@@H](N)[C@H](CO)O2)c(=O)n1`
ZINC5784279	0.791	226.2 Da LogP -1.57 TPSA 116.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@H](N)[C@@H](CO)O2)c(=O)n1`
ZINC5765920	0.773	229.2 Da LogP -0.56 TPSA 90.4	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@H](F)[C@H](CO)O2)c(=O)n1`
ZINC5765921	0.773	229.2 Da LogP -0.56 TPSA 90.4	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@H](F)[C@H](CO)O2)c(=O)n1`
ZINC43771806	0.727	243.3 Da LogP -0.16 TPSA 93.5	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=S)n1`
ZINC43771808	0.727	243.3 Da LogP -0.16 TPSA 93.5	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@@H](O)[C@@H](CO)O2)c(=S)n1`
ZINC12503923	0.723	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)c…`
ZINC12503924	0.723	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)c(…`
ZINC1532581	0.723	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(…`
ZINC3645374	0.723	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(…`
ZINC3861759	0.723	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=…`
ZINC3869816	0.723	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=…`
ZINC3869817	0.723	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3869818	0.723	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=…`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC13540919	0.694	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@H]2C[C@H](OP(=O)(O)O)[C@@H](CO)O2)c(=…`
ZINC14960489	0.694	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@@H](OP(=O)(O)O)[C@@H](CO)O2)c…`
ZINC14960497	0.694	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@H](OP(=O)(O)O)[C@@H](CO)O2)c(…`
ZINC16942629	0.694	252.2 Da LogP -0.22 TPSA 139.1	✓ Ro5	Alert	`[N-]=[N+]=N[C@H]1C[C@H](n2ccc(N)nc2=O)O[C@@H]1CO`
ZINC17142939	0.694	252.2 Da LogP -0.22 TPSA 139.1	✓ Ro5	Alert	`[N-]=[N+]=N[C@H]1C[C@H](n2ccc(N)nc2=O)O[C@H]1CO`
ZINC2522525	0.694	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@@H](OP(=O)(O)O)[C@H](CO)O2)c(…`
ZINC4543584	0.694	307.2 Da LogP -1.42 TPSA 157.1	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@H](OP(=O)(O)O)[C@H](CO)O2)c(=…`
ZINC5663881	0.694	252.2 Da LogP -0.22 TPSA 139.1	✓ Ro5	Alert	`[N-]=[N+]=N[C@H]1C[C@@H](n2ccc(N)nc2=O)O[C@H]1CO`
ZINC96031392	0.689	227.2 Da LogP -1.53 TPSA 110.6	✓ Ro5	✓ Clean	`Nc1nc(=O)ccn1[C@H]1C[C@H](O)[C@@H](CO)O1`
ZINC14960572	0.681	241.2 Da LogP -1.07 TPSA 96.6	✓ Ro5	✓ Clean	`CNc1ccn([C@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)n1`
ZINC14960580	0.681	241.2 Da LogP -1.07 TPSA 96.6	✓ Ro5	✓ Clean	`CNc1ccn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)n1`
ZINC4533800	0.680	269.3 Da LogP -0.96 TPSA 116.7	✓ Ro5	✓ Clean	`CC(=O)O[C@H]1C[C@H](n2ccc(N)nc2=O)O[C@@H]1CO`
ZINC11678823	0.667	228.2 Da LogP -2.14 TPSA 123.5	✓ Ro5	✓ Clean	`Nc1ncn([C@@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)n1`
ZINC11678826	0.667	228.2 Da LogP -2.14 TPSA 123.5	✓ Ro5	✓ Clean	`Nc1ncn([C@H]2C[C@@H](O)[C@@H](CO)O2)c(=O)n1`
ZINC1253	0.667	228.2 Da LogP -2.14 TPSA 123.5	✓ Ro5	✓ Clean	`Nc1ncn([C@@H]2C[C@@H](O)[C@H](CO)O2)c(=O)n1`
ZINC13435042	0.667	387.2 Da LogP -1.30 TPSA 203.7	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@H](O)[C@H](CO[P@](=O)(O)OP(=O…`
ZINC14960508	0.667	387.2 Da LogP -1.30 TPSA 203.7	✓ Ro5	✓ Clean	`Nc1ccn([C@@H]2C[C@H](O)[C@@H](CO[P@](=O)(O)OP(=…`
ZINC16929327	0.667	228.2 Da LogP -2.14 TPSA 123.5	✓ Ro5	✓ Clean	`Nc1ncn([C@H]2C[C@H](O)[C@@H](CO)O2)c(=O)n1`
ZINC17027370	0.667	228.2 Da LogP -2.14 TPSA 123.5	✓ Ro5	✓ Clean	`Nc1ncn([C@@H]2C[C@H](O)[C@@H](CO)O2)c(=O)n1`
ZINC8627921	0.667	228.2 Da LogP -2.14 TPSA 123.5	✓ Ro5	✓ Clean	`Nc1ncn([C@H]2C[C@H](O)[C@H](CO)O2)c(=O)n1`
ZINC8627922	0.667	228.2 Da LogP -2.14 TPSA 123.5	✓ Ro5	✓ Clean	`Nc1ncn([C@@H]2C[C@H](O)[C@H](CO)O2)c(=O)n1`
ZINC34277665	0.653	269.3 Da LogP -1.16 TPSA 113.7	✓ Ro5	✓ Clean	`CC(=O)Nc1ccn([C@@H]2C[C@@H](O)[C@H](CO)O2)c(=O)…`

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.