Protein profile

KP13_00779

Ribosomal RNA small subunit methyltransferase B

Genome: KpKP13

Gene: rsmB AHE42392.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GZ82

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Amino acids 431

Annotations 10

Features 41

PDB binders 1

Druggability 0.079

Overview

Basic information about this protein and its source genome.

Accession: KP13_00779
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rsmB AHE42392.1
Status: annotated
Amino acids: 431
Structure source: AlphaFold + ColabFold

2.1.1.176

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:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. 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:0003723 Binding to an RNA molecule or a portion thereof.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 34.483
Human E-value: 2.37e-23
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 84.848
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 96.59

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 0.079

Structure A0A0H3GZ82

Pocket Pocket 3

P2Rank 0.776

Structure A0A0H3GZ82

Pocket Pocket 1

ColabFold model

FPocket 0.155 · Pocket 7

P2Rank 0.719 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 144 / 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 9 GO

Enzyme Commission (EC)

2.1.1.176

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:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
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:0003723 Binding to an RNA molecule or a portion thereof.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0009383 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to cytosine to form 5-methylcytosine in small subunit ribosomal RNA.
GO:0070475 The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

41 records

Show feature table

Start	End	DB	Term	Name
241	426	Pfam	PF01189	16S rRNA methyltransferase RsmB/F
241	426	InterPro	IPR001678	SAM-dependent methyltransferase RsmB/NOP2-type
141	429	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
141	429	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
1	145	Gene3D	G3DSA:1.10.940.10	-
1	145	InterPro	IPR035926	NusB-like superfamily
231	429	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
231	429	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
146	172	FunFam	G3DSA:1.10.287.730:FF:000001	Ribosomal RNA small subunit methyltransferase B
173	230	FunFam	G3DSA:3.30.70.1170:FF:000002	Ribosomal RNA small subunit methyltransferase B
146	172	Gene3D	G3DSA:1.10.287.730	Helix hairpin bin
317	329	PRINTS	PR02008	RNA (C5-cytosine) methyltransferase signature
317	329	InterPro	IPR023267	RNA (C5-cytosine) methyltransferase
367	383	PRINTS	PR02008	RNA (C5-cytosine) methyltransferase signature
367	383	InterPro	IPR023267	RNA (C5-cytosine) methyltransferase
222	236	PRINTS	PR02008	RNA (C5-cytosine) methyltransferase signature
222	236	InterPro	IPR023267	RNA (C5-cytosine) methyltransferase
251	261	PRINTS	PR02008	RNA (C5-cytosine) methyltransferase signature
251	261	InterPro	IPR023267	RNA (C5-cytosine) methyltransferase
411	428	PRINTS	PR02008	RNA (C5-cytosine) methyltransferase signature
411	428	InterPro	IPR023267	RNA (C5-cytosine) methyltransferase
316	327	ProSitePatterns	PS01153	NOL1/NOP2/sun family signature.
316	327	InterPro	IPR018314	Bacterial Fmu (Sun)/eukaryotic nucleolar NOL1/Nop2p, conserved site
1	145	FunFam	G3DSA:1.10.940.10:FF:000002	Ribosomal RNA small subunit methyltransferase B
249	372	CDD	cd02440	AdoMet_MTases
5	129	CDD	cd00620	Methyltransferase_Sun
7	127	Pfam	PF01029	NusB family
7	127	InterPro	IPR006027	NusB/RsmB/TIM44
1	429	Hamap	MF_01856	Ribosomal RNA small subunit methyltransferase B [rsmB].
1	429	InterPro	IPR023541	rRNA small subunit methyltransferase B, enterobacteriaceae
173	230	Gene3D	G3DSA:3.30.70.1170	Sun protein; domain 3
164	429	ProSiteProfiles	PS51686	SAM-dependent MTase RsmB/NOP-type domain profile.
164	429	InterPro	IPR001678	SAM-dependent methyltransferase RsmB/NOP2-type
6	149	SUPERFAMILY	SSF48013	NusB-like
6	149	InterPro	IPR035926	NusB-like superfamily
117	431	PANTHER	PTHR22807	NOP2 YEAST -RELATED NOL1/NOP2/FMU SUN DOMAIN-CONTAINING
117	431	InterPro	IPR023267	RNA (C5-cytosine) methyltransferase
122	142	Coils	Coil	Coil
8	429	NCBIfam	TIGR00563	16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB
8	429	InterPro	IPR004573	rRNA small subunit methyltransferase B
234	429	FunFam	G3DSA:3.40.50.150:FF:000022	Ribosomal RNA small subunit methyltransferase B

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_A0A0H3GZ82	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00779	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	Score	Probability
1	11.85	0.628
2	2.23	0.054
3	0.82	0.003

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	11.47	0.612
2	2.02	0.044
3	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.

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
SFG	5ZVH	O57712	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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DXH	P46087	9.69	503.5 Da LogP 5.75 TPSA 97.6	2 viol.	✓ Clean	`Cc1ccc(cc1Nc2c3cnn(c3nc(n2)c4cccnc4)C)C(=O)Nc5c…`
DWT	P46087	6.44	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
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.