Protein profile

KP13_02385

23S rRNA (uracil-5-)-methyltransferase rumA

Genome: KpKP13

Gene: rumA AHE42956.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GWU7

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Amino acids 434

Annotations 8

Features 30

PDB binders 0

Druggability 0.677

Overview

Basic information about this protein and its source genome.

Accession: KP13_02385
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rumA AHE42956.1
Status: annotated
Amino acids: 434
Structure source: AlphaFold + ColabFold

2.1.1.190

GO:0008173 Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA 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:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0005506 Binding to an iron (Fe) ion. GO:0070041 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing C5-methyluridine.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 33.981
Human E-value: 1.91e-20
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 95.09

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 0.677

Structure A0A0H3GWU7

Pocket Pocket 1

P2Rank 0.634

Structure A0A0H3GWU7

Pocket Pocket 1

ColabFold model

FPocket 0.865 · Pocket 3

P2Rank 0.697 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 109 / 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 7 GO

Enzyme Commission (EC)

2.1.1.190

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: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:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0005506 Binding to an iron (Fe) ion.
GO:0070041 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing C5-methyluridine.
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.

30 records

Show feature table

Start	End	DB	Term	Name
88	432	ProSiteProfiles	PS51687	SAM-dependent methyltransferase RNA m(5)U-type domain profile.
88	432	InterPro	IPR010280	(Uracil-5)-methyltransferase family
238	426	FunFam	G3DSA:3.40.50.150:FF:000009	23S rRNA (Uracil(1939)-C(5))-methyltransferase RlmD
18	432	Hamap	MF_01010	23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD [rlmD].
18	432	InterPro	IPR001566	23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
363	393	ProSitePatterns	PS01230	RNA methyltransferase trmA family signature 1.
363	393	InterPro	IPR030390	RNA methyltransferase TrmA, active site
6	87	FunFam	G3DSA:2.40.50.140:FF:000097	23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
257	431	Pfam	PF05958	tRNA (Uracil-5-)-methyltransferase
257	431	InterPro	IPR010280	(Uracil-5)-methyltransferase family
11	66	Pfam	PF01938	TRAM domain
11	66	InterPro	IPR002792	TRAM domain
14	431	PANTHER	PTHR11061	RNA M5U METHYLTRANSFERASE
14	431	InterPro	IPR010280	(Uracil-5)-methyltransferase family
10	68	ProSiteProfiles	PS50926	TRAM domain profile.
10	68	InterPro	IPR002792	TRAM domain
24	424	NCBIfam	TIGR00479	23S rRNA (uracil-5-)-methyltransferase RlmD
1	87	Gene3D	G3DSA:2.40.50.140	-
1	87	InterPro	IPR012340	Nucleic acid-binding, OB-fold
414	424	ProSitePatterns	PS01231	RNA methyltransferase trmA family signature 2.
414	424	InterPro	IPR030391	RNA methyltransferase TrmA, conserved site
76	431	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
76	431	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
289	389	CDD	cd02440	AdoMet_MTases
128	264	Gene3D	G3DSA:2.40.50.1070	-
88	426	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
88	426	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
2	66	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
2	66	InterPro	IPR012340	Nucleic acid-binding, OB-fold
128	264	FunFam	G3DSA:2.40.50.1070:FF:000004	23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD

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_A0A0H3GWU7	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02385	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
1				0.677
6				0.47

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	8.39	0.448
2	6.46	0.326
3	2.41	0.065

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				0.865
1				0.694

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	22.93	0.884
2	1.3	0.014
3	1.2	0.011
4	1.04	0.006

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.

50 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.

No PDB ligands found through similar proteins.

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
ZINC12501520	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC115086873	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC137432264	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC144169243	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC575441396	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC1644613	0.611	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC258839852	0.611	276.3 Da LogP 0.61 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCC(F)(F)F`
ZINC167715346	0.600	266.3 Da LogP -0.18 TPSA 77.4	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCOCCCO`
ZINC34160867	0.600	222.3 Da LogP -0.20 TPSA 68.2	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCCO`
ZINC1580159	0.588	210.3 Da LogP -0.26 TPSA 58.9	✓ Ro5	✓ Clean	`OCCOCCSCCOCCO`
ZINC142610155	0.579	340.4 Da LogP -0.84 TPSA 112.9	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCOCCOCCO`
ZINC1542984426	0.579	428.5 Da LogP -0.80 TPSA 131.4	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1542984432	0.579	398.4 Da LogP -0.43 TPSA 122.1	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC207588231	0.579	207.3 Da LogP -0.75 TPSA 60.0	✓ Ro5	✓ Clean	`CNCCOCCOCCOCCO`
ZINC258828116	0.579	452.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC258836919	0.579	364.4 Da LogP -0.27 TPSA 84.8	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC33967025	0.579	252.3 Da LogP -0.87 TPSA 94.5	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCO`
ZINC39267847	0.579	208.2 Da LogP -0.89 TPSA 85.2	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCO`
ZINC575440725	0.579	295.4 Da LogP -1.03 TPSA 80.6	✓ Ro5	✓ Clean	`CN(CCOCCOCCO)CCOCCOCCO`
ZINC83254087	0.579	266.3 Da LogP -0.48 TPSA 94.5	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCO`
ZINC95920522	0.579	296.3 Da LogP -0.85 TPSA 103.7	✓ Ro5	✓ Clean	`O=C(O)COCCOCCOCCOCCOCCO`
ZINC96503406	0.579	276.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`C#CCOCCOCCOCCOCCOCCO`
ZINC96503425	0.579	222.2 Da LogP -0.50 TPSA 85.2	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCO`
ZINC96503526	0.579	442.5 Da LogP -0.41 TPSA 131.4	✓ Ro5	✓ Clean	`O=C(O)CCOCCOCCOCCOCCOCCOCCOCCOCCO`

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.