Protein profile

KP13_00539

23S rRNA (guanosine-2'-O-)-methyltransferase rlmB

Genome: KpKP13

Gene: rlmB AHE46729.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQK6

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Amino acids 243

Annotations 7

Features 23

PDB binders 2

Druggability 0.167

Overview

Basic information about this protein and its source genome.

Accession: KP13_00539
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rlmB AHE46729.1
Status: annotated
Amino acids: 243
Structure source: AlphaFold + ColabFold

2.1.1.185

GO:0008173 Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0070039 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methylguanosine.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 30.455
Human E-value: 2.58e-18
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 92.07

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 0.167

Structure A0A0H3GQK6

Pocket Pocket 3

P2Rank 0.393

Structure A0A0H3GQK6

Pocket Pocket 1

ColabFold model

FPocket 0.212 · Pocket 14

P2Rank 0.278 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 229 / 4744 genomes with a hit

Normalized 0.048

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)

2.1.1.185

Gene Ontology (GO)

GO:0008173 Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0070039 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methylguanosine.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
2	76	SUPERFAMILY	SSF55315	L30e-like
2	76	InterPro	IPR029064	50S ribosomal protein L30e-like
5	78	Pfam	PF08032	RNA 2'-O ribose methyltransferase substrate binding
5	78	InterPro	IPR013123	RNA 2-O ribose methyltransferase, substrate binding
77	243	FunFam	G3DSA:3.40.1280.10:FF:000005	23S rRNA (guanosine-2'-O-)-methyltransferase RlmB
69	242	SUPERFAMILY	SSF75217	alpha/beta knot
69	242	InterPro	IPR029028	Alpha/beta knot methyltransferases
96	236	Pfam	PF00588	SpoU rRNA Methylase family
96	236	InterPro	IPR001537	tRNA/rRNA methyltransferase, SpoU type
77	243	Gene3D	G3DSA:3.40.1280.10	-
77	243	InterPro	IPR029026	tRNA (guanine-N1-)-methyltransferase, N-terminal
1	242	NCBIfam	TIGR00186	23S rRNA (guanosine(2251)-2'-O)-methyltransferase RlmB
1	242	InterPro	IPR004441	RNA methyltransferase TrmH
2	243	Hamap	MF_01887	23S rRNA (guanosine-2'-O-)-methyltransferase RlmB [rlmB].
2	243	InterPro	IPR024915	23S rRNA (guanosine-2-O-)-methyltransferase RlmB
96	238	CDD	cd18103	SpoU-like_RlmB
1	76	FunFam	G3DSA:3.30.1330.30:FF:000007	23S rRNA methyltransferase
1	76	Gene3D	G3DSA:3.30.1330.30	-
1	76	InterPro	IPR029064	50S ribosomal protein L30e-like
2	243	PANTHER	PTHR46429	23S RRNA (GUANOSINE-2'-O-)-METHYLTRANSFERASE RLMB
2	243	InterPro	IPR004441	RNA methyltransferase TrmH
4	80	SMART	SM00967	SpoU_sub_bind_2
4	80	InterPro	IPR013123	RNA 2-O ribose methyltransferase, substrate binding

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_A0A0H3GQK6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00539	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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				4.19	0.171

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
14				0.212

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				3.37	0.12

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.

53 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
ADN	4X3M	Q5SLL8	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…`
MTA	4X3L	Q5SLL8	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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DWT	Q6IN84	7.25	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…`

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]…`
ZINC2047403	1.000	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	1.000	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	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
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]…`
ZINC3201876	1.000	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	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC3830178	1.000	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	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1O`
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…`
ZINC3978047	1.000	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	1.000	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	1.000	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	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@H](CO)[C@@H](O)[C@H]1O`
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]…`
ZINC8580514	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1O`
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…`
ZINC895113	1.000	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	1.000	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	1.000	267.2 Da LogP -1.98 TPSA 139.5	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC4188096	0.974	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188103	0.974	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC4188112	0.974	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H](…`
ZINC4188116	0.974	297.3 Da LogP -2.62 TPSA 159.8	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC101227935	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1N`
ZINC1868288	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1N`
ZINC39294072	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1N`
ZINC53204366	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1N`
ZINC57675642	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@H]1N`
ZINC57675644	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@H]1N`
ZINC57675648	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](O)[C@@H]1N`
ZINC57675649	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC71250611	0.837	266.3 Da LogP -2.01 TPSA 145.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1N`
ZINC4809089	0.833	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](S)[C@H]1O`
ZINC4809090	0.833	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](S)[C@H]1O`
ZINC4809091	0.833	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@@H](S)[C@@H]1O`
ZINC4809092	0.833	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](S)[C@@H]…`
ZINC5139067	0.829	283.3 Da LogP -1.04 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CS)[C@@H](O)[C@H]1O`
ZINC105358492	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@@H]1F`
ZINC22805	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@@H]1F`
ZINC2383767290	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@H](O)[C@@H]1F`
ZINC3827883	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@H]1F`
ZINC5163038	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@@H](O)[C@H]1F`
ZINC5372462	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@@H](CO)[C@@H](O)[C@@H]…`
ZINC66155300	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@@H]1O[C@H](CO)[C@H](O)[C@H]1F`
ZINC83323919	0.818	269.2 Da LogP -1.00 TPSA 119.3	✓ Ro5	✓ Clean	`Nc1ncnc2c1ncn2[C@H]1O[C@@H](CO)[C@H](O)[C@@H]1F`

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.