Protein profile

KP13_03862

Ribosomal RNA large subunit methyltransferase E

Genome: KpKP13

Gene: rlmL AHE45391.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GL44

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Amino acids 701

Annotations 9

Features 35

PDB binders 1

Druggability 0.273

Overview

Basic information about this protein and its source genome.

Accession: KP13_03862
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rlmL AHE45391.1
Status: annotated
Amino acids: 701
Structure source: AlphaFold + ColabFold

GO:0008990 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0031167 The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule. GO:0003676 Binding to a nucleic acid. GO:0032259 The process in which a methyl group is covalently attached to a 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: 92.25

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 0.273

Structure A0A0H3GL44

Pocket Pocket 49

P2Rank 0.863

Structure A0A0H3GL44

Pocket Pocket 1

ColabFold model

FPocket 0.393 · Pocket 9

P2Rank 0.796 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 139 / 4744 genomes with a hit

Normalized 0.029

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Gene Ontology (GO)

GO:0008990 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0031167 The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
GO:0003676 Binding to a nucleic acid.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.
GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0052915 Catalysis of the reaction: S-adenosyl-L-methionine + guanosine(2445) in 23S rRNA = N(2)-methylguanosine(2445) in 23S rRNA + S-adenosyl-L-homocysteine.
GO:0070043 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N7-methylguanine.

Sequence Features

Domain/signature hits from InterPro and related databases.

35 records

Show feature table

Start	End	DB	Term	Name
483	701	FunFam	G3DSA:3.40.50.150:FF:000039	Ribosomal RNA large subunit methyltransferase K/L
456	657	Pfam	PF10672	S-adenosylmethionine-dependent methyltransferase
456	657	InterPro	IPR019614	S-adenosylmethionine-dependent methyltransferase
146	373	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
146	373	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
24	156	CDD	cd11715	THUMP_AdoMetMT
56	154	SMART	SM00981	THUMP_a_2
56	154	InterPro	IPR004114	THUMP domain
195	206	ProSitePatterns	PS01261	Uncharacterized protein family UPF0020 signature.
195	206	InterPro	IPR000241	Ribosomal RNA large subunit methyltransferase K/L-like, FLD domain
160	372	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
160	372	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
1	701	PIRSF	PIRSF037618	RNA_Mtase_bacterial
1	701	InterPro	IPR017244	Ribosomal RNA large subunit methyltransferase K/L
6	246	Gene3D	G3DSA:3.30.2130.30	-
306	312	ProSitePatterns	PS00092	N-6 Adenine-specific DNA methylases signature.
306	312	InterPro	IPR002052	DNA methylase, N-6 adenine-specific, conserved site
4	701	Hamap	MF_01858	Ribosomal RNA large subunit methyltransferase K/L [rlmL].
4	701	InterPro	IPR017244	Ribosomal RNA large subunit methyltransferase K/L
483	701	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
483	701	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
394	697	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
394	697	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
540	654	CDD	cd02440	AdoMet_MTases
162	375	Pfam	PF01170	Putative RNA methylase family UPF0020
162	375	InterPro	IPR000241	Ribosomal RNA large subunit methyltransferase K/L-like, FLD domain
391	482	Gene3D	G3DSA:3.30.750.80	RNA methyltransferase domain (HRMD) like
2	458	PANTHER	PTHR47313	RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE K/L
23	153	Pfam	PF02926	THUMP domain
23	153	InterPro	IPR004114	THUMP domain
43	154	ProSiteProfiles	PS51165	THUMP domain profile.
43	154	InterPro	IPR004114	THUMP domain
303	315	PRINTS	PR00507	N12 class N6 adenine-specific DNA methyltransferase signature
193	207	PRINTS	PR00507	N12 class N6 adenine-specific DNA methyltransferase signature
391	482	FunFam	G3DSA:3.30.750.80:FF:000001	Ribosomal RNA large subunit methyltransferase K/L

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_A0A0H3GL44	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03862	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
49				0.273

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	16.62	0.782
2	7.21	0.375
3	6.0	0.295
4	5.2	0.241
5	1.9	0.038

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
9				0.393

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	13.92	0.704
2	6.59	0.334
3	5.58	0.267
4	4.13	0.167
5	3.64	0.137

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
SFG	3TM5	Q8U248	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.