Protein profile

KP13_02027

Ribosomal RNA small subunit methyltransferase C

Genome: KpKP13

Gene: AHE46463.1 rsmC Structure source: AlphaFold + ColabFold UniProt A0A0H3GIT7

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Amino acids 342

Annotations 10

Features 17

PDB binders 5

Druggability 0.394

Overview

Basic information about this protein and its source genome.

Accession: KP13_02027
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE46463.1 rsmC
Status: annotated
Amino acids: 342
Structure source: AlphaFold + ColabFold

2.1.1.172

GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0008990 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine. GO:0003676 Binding to a nucleic acid. GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. GO:0032259 The process in which a methyl group is covalently attached to a molecule. 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.

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: 94.51

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 0.394

Structure A0A0H3GIT7

Pocket Pocket 4

P2Rank 0.867

Structure A0A0H3GIT7

Pocket Pocket 1

ColabFold model

FPocket 0.235 · Pocket 3

P2Rank 0.847 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 107 / 4744 genomes with a hit

Normalized 0.023

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)

2.1.1.172

Gene Ontology (GO)

GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0008990 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N2-methylguanine.
GO:0003676 Binding to a nucleic acid.
GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.
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:0008757 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0052914 Catalysis of the reaction: S-adenosyl-L-methionine + guanosine(1207) in 16S rRNA = N(2)-methylguanosine(1207) in 16S rRNA + S-adenosyl-L-homocysteine.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records

Show feature table

Start	End	DB	Term	Name
159	342	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
159	342	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
4	336	Hamap	MF_01862	Ribosomal RNA small subunit methyltransferase C [rsmC].
4	336	InterPro	IPR023543	rRNA small subunit methyltransferase C
4	336	PANTHER	PTHR47816	RIBOSOMAL RNA SMALL SUBUNIT METHYLTRANSFERASE C
4	336	InterPro	IPR046977	rRNA (guanine-N(2)-)-methyltransferase RsmC/RlmG
199	299	CDD	cd02440	AdoMet_MTases
265	271	ProSitePatterns	PS00092	N-6 Adenine-specific DNA methylases signature.
265	271	InterPro	IPR002052	DNA methylase, N-6 adenine-specific, conserved site
167	333	Pfam	PF05175	Methyltransferase small domain
167	333	InterPro	IPR007848	Methyltransferase small domain
1	158	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
1	158	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
107	325	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
107	325	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
8	162	Pfam	PF08468	Methyltransferase small domain N-terminal
8	162	InterPro	IPR013675	Methyltransferase small, N-terminal

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_A0A0H3GIT7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02027	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
4				0.394

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	14.62	0.728
2	3.51	0.129
3	1.56	0.024
4	1.01	0.006

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
3				0.235

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	12.86	0.665
2	3.0	0.098
3	1.8	0.034
4	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.

55 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
7QM	5U1I	Q2MG72	497.5 Da LogP -7.06 TPSA 274.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H]([C@H](O[C@@H]([C@@H]1O)O[C@H]2[C…`
7XP	5U0N	Q2MG72	454.5 Da LogP -6.65 TPSA 262.4	2 viol.	✓ Clean	`C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C…`
827	5U19	Q2MG72	482.5 Da LogP -6.00 TPSA 248.4	2 viol.	✓ Clean	`C[C@@]1(CO[C@@H]([C@@H]([C@H]1NC)O)O[C@H]2[C@@H…`
9CS	5U1E	Q2MG72	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`C1[C@@H]([C@H]([C@@H]([C@H]([C@@H]1N)O[C@@H]2[C…`
GET	5U18	Q2MG72	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`C[C@H]([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O[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
ZINC100069123	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](O)[C@H](O[…`
ZINC106588639	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@@H](…`
ZINC1772820029	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H]…`
ZINC1857790211	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@…`
ZINC1857790212	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@…`
ZINC252460108	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@@H](…`
ZINC253380792	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@@H]2[C@H](N)C[C@H](N…`
ZINC253380793	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@@H]2[C@H](N)C[C@H](N…`
ZINC253380794	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@H]2[C@@H](O)[C@@H](O…`
ZINC253380795	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@H](O[C@H]2[C@@H](O)[C@@H](O…`
ZINC256001609	1.000	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC256001610	1.000	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC256001611	1.000	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC256001612	1.000	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@@H]2[C@H](N)C[C@H](N)[C@H](…`
ZINC43543817	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H]…`
ZINC49708768	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H]…`
ZINC53132258	1.000	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC60183639	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC60183641	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC60183644	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC60183647	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@H]2[C@@H](N)C[C@@H]…`
ZINC60184326	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](O)[C@H](O[…`
ZINC64857811	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@@H](O)[C@@H](O[C@@H]2[C@@H](O)[C@H](…`
ZINC70691602	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@H]…`
ZINC70691603	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@H]…`
ZINC70691604	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@@H](…`
ZINC70691605	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@H](O[C@@H]2[C@@H](N)C[C@@H](…`
ZINC72332859	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@H]…`
ZINC72332860	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@H]1[C@H](O)[C@@H](O[C@@H]2[C@@H](N)C[C@@H]…`
ZINC77301567	1.000	483.5 Da LogP -7.33 TPSA 288.4	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@H]2[C@H](N)C[C@H](N)[C@@H](O…`
ZINC936069019	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@H](N)C[C@H](…`
ZINC936069020	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@H](N)C[C@H](…`
ZINC936069021	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@H](N)C[C@H](…`
ZINC936069022	1.000	496.6 Da LogP -5.61 TPSA 248.4	2 viol.	✓ Clean	`CN[C@@H]1[C@H](O)[C@@H](O[C@@H]2[C@H](N)C[C@H](…`
ZINC17654095	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@…`
ZINC1857793042	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC239203291	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC239203292	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@@H]3…`
ZINC242649355	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649360	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC242649362	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](N)C[C@@H](N)[C@H]…`
ZINC245224173	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224174	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC245224175	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@@H](O[C@@H]2[C@H](N)C[C@H](N)[C@@H…`
ZINC43470138	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H…`
ZINC8101132	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@H]3O…`
ZINC8101133	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](O[C@H]3O…`
ZINC8101134	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@H](O[C@H]3O[…`
ZINC8101135	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@H](O[C@H]3O[…`
ZINC8214590	0.878	484.5 Da LogP -7.29 TPSA 282.6	2 viol.	✓ Clean	`NC[C@H]1O[C@H](O[C@@H]2[C@@H](N)C[C@@H](N)[C@H]…`

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.