Protein profile

KP13_00215

putative tRNA/rRNA methyltransferase

Genome: KpKP13

Gene: AHE42128.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GXA6

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Amino acids 157

Annotations 12

Features 16

PDB binders 1

Druggability 0.475

Overview

Basic information about this protein and its source genome.

Accession: KP13_00215
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42128.1
Status: annotated
Amino acids: 157
Structure source: AlphaFold + ColabFold

2.1.1.207

GO:0001510 Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor. GO:0008173 Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule. GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 44.079
DEG E-value: 6.57e-41
Localization: Unknown
ColabFold pLDDT: 93.54

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 0.475

Structure A0A0H3GXA6

Pocket Pocket 2

P2Rank 0.309

Structure A0A0H3GXA6

Pocket Pocket 1

ColabFold model

FPocket 0.293 · Pocket 1

P2Rank 0.562 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 461 / 4744 genomes with a hit

Normalized 0.097

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

2.1.1.207

Gene Ontology (GO)

GO:0001510 Posttranscriptional addition of a methyl group to either a nucleotide or 2'-O ribose in a polyribonucleotide. Usually uses S-adenosylmethionine as a cofactor.
GO:0008173 Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0042802 Binding to an identical protein or proteins.
GO:0141102 Catalysis of the reaction: 5-carboxymethylaminomethyluridine34 in tRNA(Leu) + S-adenosyl-L-methionine = 5-carboxymethylaminomethyl-2'-O-methyluridine34 in tRNA(Leu) + H+ + S-adenosyl-L-homocysteine.
GO:0141098 Catalysis of the reaction: cytidine(34) in tRNA + S-adenosyl-L-methionine = 2'-O-methylcytidine(34) in tRNA + H+ + S-adenosyl-L-homocysteine.
GO:0002131 The process in which the ribose of cytidine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'-O position.
GO:0002132 The process in which the ribose of uridine at position 34 in the anticodon of a tRNA is post-transcriptionally methylated at the 2'-O position.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
1	152	SUPERFAMILY	SSF75217	alpha/beta knot
1	152	InterPro	IPR029028	Alpha/beta knot methyltransferases
1	154	PIRSF	PIRSF029256	SpoU_TrmH
1	154	InterPro	IPR016914	tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL
1	157	Gene3D	G3DSA:3.40.1280.10	-
1	157	InterPro	IPR029026	tRNA (guanine-N1-)-methyltransferase, N-terminal
1	153	PANTHER	PTHR42971	TRNA (CYTIDINE(34)-2'-O)-METHYLTRANSFERASE
1	153	InterPro	IPR016914	tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL
2	142	Pfam	PF00588	SpoU rRNA Methylase family
2	142	InterPro	IPR001537	tRNA/rRNA methyltransferase, SpoU type
3	148	CDD	cd18094	SpoU-like_TrmL
3	148	InterPro	IPR016914	tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL
1	153	NCBIfam	TIGR00185	tRNA (uridine(34)/cytosine(34)/5-carboxymethylaminomethyluridine(34)-2'-O)-methyltransferase TrmL
1	154	FunFam	G3DSA:3.40.1280.10:FF:000002	Peptidylprolyl isomerase
2	151	Hamap	MF_01885	tRNA (cytidine(34)-2'-O)-methyltransferase [trmL].
2	151	InterPro	IPR016914	tRNA (cytidine/uridine-2'-O-)-methyltransferase TrmL

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_A0A0H3GXA6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00215	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
2				0.475
1				0.186
3				0.004
5				0.004

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				7.11	0.309

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				0.293

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				6.8	0.348
2				0.93	0.004

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
MTA	5CO4	Q72G96	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)…`

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
ZINC100349915	1.000	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H…`
ZINC105279440	1.000	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]1O`
ZINC12501834	1.000	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@…`
ZINC1318753	1.000	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]…`
ZINC25963247	1.000	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]…`
ZINC3869319	1.000	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H…`
ZINC4228245	1.000	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H…`
ZINC5929300	1.000	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]…`
ZINC895091	1.000	297.3 Da LogP -0.61 TPSA 119.3	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H…`
ZINC253500647	0.766	298.3 Da LogP -0.49 TPSA 113.5	✓ Ro5	✓ Clean	`CSC[C@@H]1O[C@H](n2cnc3c(O)ncnc32)[C@H](O)[C@H]…`
ZINC5139067	0.756	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CS)[C@@H](O)[C@H]1O`
ZINC14766197	0.745	339.4 Da LogP 0.42 TPSA 119.3	✓ Ro5	✓ Clean	`CC(C)CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O…`
ZINC201682330	0.745	339.4 Da LogP 0.42 TPSA 119.3	✓ Ro5	✓ Clean	`CC(C)CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)…`
ZINC248157271	0.745	339.4 Da LogP 0.42 TPSA 119.3	✓ Ro5	✓ Clean	`CC(C)CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)…`
ZINC2516140	0.745	339.4 Da LogP 0.42 TPSA 119.3	✓ Ro5	✓ Clean	`CC(C)CSC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O…`
ZINC5138266	0.745	339.4 Da LogP 0.42 TPSA 119.3	✓ Ro5	✓ Clean	`CC(C)CSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)…`
ZINC2047403	0.739	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	0.739	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	0.739	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	0.739	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	0.739	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC3814316	0.739	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]…`
ZINC3830178	0.739	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	0.739	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	0.739	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	0.739	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	0.739	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	0.739	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
ZINC4773848	0.739	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H]…`
ZINC4773849	0.739	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@@H…`
ZINC4773850	0.739	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@H…`
ZINC4773851	0.739	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@@…`
ZINC77981211	0.739	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](O)[C@H]…`
ZINC82228511	0.739	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`NC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C@H]1O`
ZINC8580514	0.739	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	0.739	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	0.739	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	0.739	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC1081541	0.723	285.7 Da LogP -0.73 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CCl)[C@@H](O)[C@@H]…`
ZINC4188096	0.723	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188103	0.723	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC4188112	0.723	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188116	0.723	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC5941240	0.723	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CF)[C@@H](O)[C@H]1O`
ZINC5163039	0.712	340.4 Da LogP -0.89 TPSA 145.3	✓ Ro5	✓ Clean	`NCCCSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@H](O)[C…`
ZINC73315766	0.704	381.5 Da LogP 1.73 TPSA 119.3	✓ Ro5	✓ Clean	`CCCCCCCSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](…`
ZINC73315769	0.704	381.5 Da LogP 1.73 TPSA 119.3	✓ Ro5	✓ Clean	`CCCCCCCSC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H]…`
ZINC73315770	0.704	381.5 Da LogP 1.73 TPSA 119.3	✓ Ro5	✓ Clean	`CCCCCCCSC[C@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H](…`
ZINC73315774	0.704	381.5 Da LogP 1.73 TPSA 119.3	✓ Ro5	✓ Clean	`CCCCCCCSC[C@@H]1O[C@@H](n2cnc3c(N)ncnc32)[C@@H]…`
ZINC256828117	0.698	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)[…`

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.