Target Pathogen

Overview

Basic information about this protein and its source genome.

Accession: KP13_01581
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rlmA AHE43894.1
Status: annotated
Amino acids: 225
Structure source: ColabFold

GO

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 (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 91.01

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 0.852

Structure CB_KP13_01581

Pocket Pocket 1

P2Rank 0.864

Structure CB_KP13_01581

Pocket Pocket 1

ColabFold model

FPocket 0.852 · Pocket 1

P2Rank 0.864 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 117 / 4744 genomes with a hit

Normalized 0.025

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1

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

Sequence Features

Domain/signature hits from InterPro and related databases.

8 records

Show feature table

Start	End	DB	Term	Name
5	207	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
5	207	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
1	225	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
1	225	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
22	198	PANTHER	PTHR43460	METHYLTRANSFERASE
48	131	Pfam	PF08241	Methyltransferase domain
48	131	InterPro	IPR013216	Methyltransferase type 11
46	132	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 + 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 KP13_01581	ColabFold	—	—	full sequence	—	Viewing

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				0.852

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				15.57	0.756

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.

12 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
TEX	5GM2	A0A077K7L1	437.6 Da LogP 4.85 TPSA 68.4	✓ Ro5	Alert	`CC(C)[C@H]1C(=O)N[C@@H](Cc2c[nH]c3c2c(ccc3[C@](…`

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
ZINC2383097	1.000	437.6 Da LogP 4.85 TPSA 68.4	✓ Ro5	Alert	`C=C[C@](C)(CCC=C(C)C)c1ccc2c3c(c[nH]c13)C[C@@H]…`
ZINC31333229	1.000	437.6 Da LogP 4.85 TPSA 68.4	✓ Ro5	Alert	`C=C[C@@](C)(CCC=C(C)C)c1ccc2c3c(c[nH]c13)C[C@@H…`
ZINC3873176	1.000	437.6 Da LogP 4.85 TPSA 68.4	✓ Ro5	Alert	`C=C[C@](C)(CCC=C(C)C)c1ccc2c3c(c[nH]c13)C[C@@H]…`
ZINC3873177	1.000	437.6 Da LogP 4.85 TPSA 68.4	✓ Ro5	Alert	`C=C[C@](C)(CCC=C(C)C)c1ccc2c3c(c[nH]c13)C[C@H](…`
ZINC3873178	1.000	437.6 Da LogP 4.85 TPSA 68.4	✓ Ro5	Alert	`C=C[C@](C)(CCC=C(C)C)c1ccc2c3c(c[nH]c13)C[C@H](…`
ZINC104949681	0.787	453.6 Da LogP 3.82 TPSA 88.6	✓ Ro5	Alert	`C=C[C@](C)(CC[C@H](O)C(=C)C)c1ccc2c3c(c[nH]c13)…`
ZINC104949684	0.787	453.6 Da LogP 3.82 TPSA 88.6	✓ Ro5	Alert	`C=C[C@](C)(CC[C@H](O)C(=C)C)c1ccc2c3c(c[nH]c13)…`
ZINC104949689	0.787	453.6 Da LogP 3.82 TPSA 88.6	✓ Ro5	Alert	`C=C[C@](C)(CC[C@H](O)C(=C)C)c1ccc2c3c(c[nH]c13)…`
ZINC104949693	0.787	453.6 Da LogP 3.82 TPSA 88.6	✓ Ro5	Alert	`C=C[C@](C)(CC[C@H](O)C(=C)C)c1ccc2c3c(c[nH]c13)…`
ZINC2517049	0.569	301.4 Da LogP 1.66 TPSA 68.4	✓ Ro5	✓ Clean	`CC(C)[C@H]1C(=O)N[C@H](CO)Cc2c[nH]c3cccc(c23)N1C`
ZINC57363	0.569	301.4 Da LogP 1.66 TPSA 68.4	✓ Ro5	✓ Clean	`CC(C)[C@@H]1C(=O)N[C@@H](CO)Cc2c[nH]c3cccc(c23)…`

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.