Protein profile

KP13_04048

Phage DNA adenine methylase

Genome: KpKP13

Gene: AHE45152.1 Structure source: AlphaFold + ColabFold UniProt A0A486V7D8

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Amino acids 349

Annotations 7

Features 19

PDB binders 2

Druggability 0.868

Overview

Basic information about this protein and its source genome.

Accession: KP13_04048
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE45152.1
Status: annotated
Amino acids: 349
Structure source: AlphaFold + ColabFold

2.1.1.-

GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0006306 OBSOLETE. The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine. GO:0003676 Binding to a nucleic acid. GO:0032259 The process in which a methyl group is covalently attached to a molecule. GO:0008170 Catalysis of the transfer of a methyl group to the nitrogen atom of an acceptor molecule. GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

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 (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 88.39

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 0.868

Structure A0A486V7D8

Pocket Pocket 1

P2Rank 0.782

Structure A0A486V7D8

Pocket Pocket 1

ColabFold model

FPocket 0.91 · Pocket 1

P2Rank 0.815 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 12 / 4744 genomes with a hit

Normalized 0.003

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)

2.1.1.-

Gene Ontology (GO)

GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0006306 OBSOLETE. The covalent transfer of a methyl group to either N-6 of adenine or C-5 or N-4 of cytosine.
GO:0003676 Binding to a nucleic acid.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.
GO:0008170 Catalysis of the transfer of a methyl group to the nitrogen atom of an acceptor molecule.
GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
32	38	ProSitePatterns	PS00092	N-6 Adenine-specific DNA methylases signature.
32	38	InterPro	IPR002052	DNA methylase, N-6 adenine-specific, conserved site
8	348	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
8	348	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
29	341	Pfam	PF01555	DNA methylase
29	341	InterPro	IPR002941	DNA methylase N-4/N-6
10	345	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
10	345	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
325	345	PRINTS	PR00508	S21 class N4 adenine-specific DNA methyltransferase signature
325	345	InterPro	IPR001091	Restriction/modification DNA-methyltransferase
63	83	PRINTS	PR00508	S21 class N4 adenine-specific DNA methyltransferase signature
63	83	InterPro	IPR001091	Restriction/modification DNA-methyltransferase
283	300	PRINTS	PR00508	S21 class N4 adenine-specific DNA methyltransferase signature
283	300	InterPro	IPR001091	Restriction/modification DNA-methyltransferase
302	320	PRINTS	PR00508	S21 class N4 adenine-specific DNA methyltransferase signature
302	320	InterPro	IPR001091	Restriction/modification DNA-methyltransferase
28	42	PRINTS	PR00508	S21 class N4 adenine-specific DNA methyltransferase signature
28	42	InterPro	IPR001091	Restriction/modification DNA-methyltransferase
6	79	CDD	cd02440	AdoMet_MTases

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 + 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_A0A486V7D8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_04048	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
1				0.868

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	Score	Probability
1	12.24	0.644
2	7.41	0.388
3	5.83	0.285
4	1.45	0.02
5	1.29	0.014

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
1				0.91

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	Score	Probability
1	13.48	0.688
2	5.0	0.227
3	3.77	0.145
4	2.57	0.073

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.

52 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
MTA	1EG2	P14751	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)…`
SFG	6PBD	P0CAW2	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)…`

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
ZINC13650200	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…`
ZINC205994753	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…`
ZINC205994774	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…`
ZINC27723577	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@H](N)…`
ZINC38192471	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@H](N)CC[C@@H](N…`
ZINC38192472	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@@H](N)CC[C@@H](…`
ZINC4217451	1.000	381.4 Da LogP -2.06 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[C@@H](N)CC[C@H](N…`
ZINC13522400	0.737	400.4 Da LogP -2.42 TPSA 199.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[S@](=O)CC[C@H](N)…`
ZINC13522403	0.737	400.4 Da LogP -2.42 TPSA 199.7	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C[S@@](=O)CC[C@H](N…`
ZINC13522378	0.732	370.4 Da LogP -1.83 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…`
ZINC13522407	0.732	370.4 Da LogP -1.83 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…`
ZINC256828117	0.732	370.4 Da LogP -1.83 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…`
ZINC256828118	0.732	370.4 Da LogP -1.83 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSC[C@H](N)C(=O)O)[…`
ZINC1775937521	0.726	423.5 Da LogP -1.02 TPSA 194.7	2 viol.	✓ Clean	`CCCN[C@H](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc…`
ZINC95921230	0.726	423.5 Da LogP -1.02 TPSA 194.7	2 viol.	✓ Clean	`CCCN[C@@H](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cn…`
ZINC12501055	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…`
ZINC13509082	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CSCC[C@@H](N)C(=O)O…`
ZINC13509104	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@@H](N)C(=O)O…`
ZINC1532516	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CSCC[C@H](N)C(=O)O)…`
ZINC33821012	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…`
ZINC33821013	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…`
ZINC4228232	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CSCC[C@H](N)C(=O)O)…`
ZINC45789230	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CSCC[C@H](N)C(=O)O…`
ZINC45789233	0.724	384.4 Da LogP -1.44 TPSA 182.6	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CSCC[C@H](N)C(=O)O)[…`
ZINC49014951	0.724	416.4 Da LogP -2.76 TPSA 216.8	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CS(=O)(=O)CC[C@H](N)…`
ZINC49014955	0.724	416.4 Da LogP -2.76 TPSA 216.8	1 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CS(=O)(=O)CC[C@@H](N…`
ZINC100005972	0.712	400.5 Da LogP -1.54 TPSA 182.6	1 viol.	✓ Clean	`C[S@@H](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC12371977	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC12371978	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…`
ZINC13522357	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3…`
ZINC13522362	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC139339614	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c…`
ZINC254297245	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c(…`
ZINC254297254	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c(…`
ZINC254297257	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c(…`
ZINC33821030	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC33821031	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…`
ZINC4214738	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC4228231	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…`
ZINC71755544	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3c…`
ZINC71755557	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@@H](N)C(=O)O)C[C@@H]1O[C@H](n2cnc3…`
ZINC95644663	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c…`
ZINC95644664	0.700	399.5 Da LogP -1.92 TPSA 182.6	✓ Ro5	✓ Clean	`C[S@+](CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc3c(…`
ZINC5139067	0.654	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CS)[C@@H](O)[C@H]1O`
ZINC4513750	0.648	281.2 Da LogP -1.89 TPSA 156.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](C(=O)O)[C@@H](O)[C@…`
ZINC4513754	0.648	281.2 Da LogP -1.89 TPSA 156.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](C(=O)O)[C@@H](O)[C…`
ZINC4513757	0.648	281.2 Da LogP -1.89 TPSA 156.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](C(=O)O)[C@@H](O)[C@…`
ZINC4513760	0.648	281.2 Da LogP -1.89 TPSA 156.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](C(=O)O)[C@@H](O)[C…`
ZINC5163034	0.648	281.2 Da LogP -1.89 TPSA 156.6	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](C(=O)O)[C@@H](O)[C@…`
ZINC13551750	0.645	379.4 Da LogP -1.94 TPSA 208.6	2 viol.	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O/C(=C\[C@@H](N)CC[C@@H](N…`

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.