Protein profile

KP13_00306

DNA methylase, N-6 adenine-specific protein

Genome: KpKP13

Gene: AHE42215.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GX18

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Amino acids 280

Annotations 9

Features 13

PDB binders 2

Druggability 0.946

Overview

Basic information about this protein and its source genome.

Accession: KP13_00306
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42215.1
Status: annotated
Amino acids: 280
Structure source: AlphaFold + ColabFold

2.1.1.266

GO:0070475 The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule. GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0003676 Binding to a nucleic acid. GO:0032259 The process in which a methyl group is covalently attached to a molecule. GO:0008649 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule. The methyl group can be transfered to the nucleobase or to the ribose group of the nucleoside. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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: 94.72

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 0.946

Structure A0A0H3GX18

Pocket Pocket 1

P2Rank 0.724

Structure A0A0H3GX18

Pocket Pocket 1

ColabFold model

FPocket 0.469 · Pocket 1

P2Rank 0.725 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 140 / 4744 genomes with a hit

Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

2.1.1.266

Gene Ontology (GO)

GO:0070475 The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0003676 Binding to a nucleic acid.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.
GO:0008649 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule. The methyl group can be transfered to the nucleobase or to the ribose group of the nucleoside.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0036307 Catalysis of the reaction: S-adenosyl-L-methionine + adenine(2030) in 23S rRNA = S-adenosyl-L-homocysteine + rRNA containing N(6)-methyladenine(2030) in 23S rRNA.
GO:0003723 Binding to an RNA molecule or a portion thereof.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
2	266	Hamap	MF_00934	Ribosomal RNA large subunit methyltransferase J [rlmJ].
2	266	InterPro	IPR007473	Ribosomal RNA large subunit methyltransferase J
1	280	FunFam	G3DSA:3.40.50.150:FF:000037	Ribosomal RNA large subunit methyltransferase J
1	280	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
1	280	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
9	279	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
9	279	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
241	247	ProSitePatterns	PS00092	N-6 Adenine-specific DNA methylases signature.
241	247	InterPro	IPR002052	DNA methylase, N-6 adenine-specific, conserved site
33	278	Pfam	PF04378	Ribosomal RNA large subunit methyltransferase D, RlmJ
33	278	InterPro	IPR007473	Ribosomal RNA large subunit methyltransferase J
1	280	PANTHER	PTHR37426	RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE J
1	280	InterPro	IPR007473	Ribosomal RNA large subunit methyltransferase J

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_A0A0H3GX18	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00306	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				0.946

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				21.25	0.867
2				1.47	0.02

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				0.469
2				0.25

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	11.92	0.631
2	4.76	0.21
3	2.95	0.095
4	1.75	0.032

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
HY8	6QDX	P37634	674.7 Da LogP -3.61 TPSA 311.4	3 viol.	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@@H](O3…`
HZ2	6QE0	P37634	660.6 Da LogP -4.00 TPSA 311.4	3 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
ZINC584905214	0.726	452.5 Da LogP -1.92 TPSA 189.1	1 viol.	✓ Clean	`CN(C)CCCN(CC[C@H](N)C(=O)O)C[C@H]1O[C@@H](n2cnc…`
ZINC11582480	0.597	339.3 Da LogP -1.68 TPSA 162.8	✓ Ro5	✓ Clean	`O=C(O)CCNc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O…`
ZINC12656099	0.597	339.3 Da LogP -1.68 TPSA 162.8	✓ Ro5	✓ Clean	`O=C(O)CCNc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O…`
ZINC1782261	0.597	339.3 Da LogP -1.68 TPSA 162.8	✓ Ro5	✓ Clean	`O=C(O)CCNc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)…`
ZINC247417127	0.597	339.3 Da LogP -1.68 TPSA 162.8	✓ Ro5	✓ Clean	`O=C(O)CCNc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)…`
ZINC105064588	0.594	311.3 Da LogP -2.16 TPSA 145.8	✓ Ro5	✓ Clean	`OCCNc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]…`
ZINC14451064	0.594	311.3 Da LogP -2.16 TPSA 145.8	✓ Ro5	✓ Clean	`OCCNc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@…`
ZINC1685071	0.594	311.3 Da LogP -2.16 TPSA 145.8	✓ Ro5	✓ Clean	`OCCNc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@…`
ZINC27414326	0.594	311.3 Da LogP -2.16 TPSA 145.8	✓ Ro5	✓ Clean	`OCCNc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H…`
ZINC27414327	0.594	311.3 Da LogP -2.16 TPSA 145.8	✓ Ro5	✓ Clean	`OCCNc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H…`
ZINC4722772	0.594	311.3 Da LogP -2.16 TPSA 145.8	✓ Ro5	✓ Clean	`OCCNc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H…`
ZINC4722773	0.594	311.3 Da LogP -2.16 TPSA 145.8	✓ Ro5	✓ Clean	`OCCNc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@…`
ZINC4722774	0.594	311.3 Da LogP -2.16 TPSA 145.8	✓ Ro5	✓ Clean	`OCCNc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@…`
ZINC6119248	0.594	311.3 Da LogP -2.16 TPSA 145.8	✓ Ro5	✓ Clean	`OCCNc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H…`
ZINC1319874	0.581	353.4 Da LogP -1.13 TPSA 145.8	✓ Ro5	✓ Clean	`C[C@H](CO)CCNc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@…`
ZINC13782061	0.581	353.4 Da LogP -1.13 TPSA 145.8	✓ Ro5	✓ Clean	`C[C@@H](CO)CCNc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@…`
ZINC13650200	0.568	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	0.568	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	0.568	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	0.568	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	0.568	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	0.568	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	0.568	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…`
ZINC2047403	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1O`
ZINC2047673	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC2169830	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC3201876	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC3201878	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC3830178	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3830179	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
ZINC3978047	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC3978048	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC3978049	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1O`
ZINC4048240	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC8580514	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC895113	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC896706	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC970363	0.567	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC13522400	0.560	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	0.560	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…`
ZINC4188096	0.559	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188103	0.559	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC4188112	0.559	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188116	0.559	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC12501055	0.553	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	0.553	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	0.553	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	0.553	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	0.553	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	0.553	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…`

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.