KpATCC43816 Protein target profile

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

Accession: VK055_4387

Gene: rumA AIK82930.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GWU7
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Length 434
Pocket druggability (P2Rank · AlphaFold DB model) 0.634
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 50 total records
Functional annotation 1 EC 7 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.68. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.63. Review the complete evidence below

Risks to review

Human similarity Top human hit identity: 34.555%. This target also has a predicted binding pocket (P2Rank 0.63) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 108 of 4744 screened genomes (2.3%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.63) — check the ligand evidence before deprioritizing on off-target risk alone. Only proposed compounds 50 ZINC similarity-based candidates, no stronger ligand evidence.

Evidence coverage

Core evidence streams are available for this target.
Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
34.555 Lower values reduce human off-target concern.
Human E-value
4.9e-20
Gut microbiome similarity
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
28.448 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
95.22 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.634
Structure A0A0H3GWU7
Pocket Pocket 1
Druggability (FPocket) 0.677
Structure A0A0H3GWU7
Pocket Pocket 1
ColabFold model
P2Rank 0.908 · Pocket 1
FPocket 0.832 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 108 / 4744 genomes with a hit
Prevalence 2.3%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network
Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MAQFYSAKRRVTTRQIITVTVNDLDPFGQGVARHQGKALFVSGVLPHEQAEVALVEDKKQYARAEVKRRLTDSPQRQAPRCPHFGVCGGCQQQHASVPLQQQSKRAALGRLMKREVDDVIAGAPWGYRRRARLSLNYQPKTQQLQMGFRQANAKAIVDVVQCPVLVPQLEALLPAVRECLSALSALRHLGHVELVQADNGPLMVLRHTAALPATDREKLERFSQTHGLSLYLAPQSEILEQIHGEAPWYTSDGLRLVFSPRDFIQVNDGVNQQMVRTALEWLDLRPEDRVLDLFCGMGNFTLPLATRAAHVVGVEGVPALVEKGRENAARNGLSNVTFFHENLEEDVTRQAWAKHGFDKVLLDPARAGAPGVMPHIIKLAPRRVVYVSCNPATLARDSETLLQAGYQIQRLAMLDMFPHTGHLESMVLFERRLT

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
  • 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: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 domains and features

Domain and signature matches imported from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
128 264 FunFam G3DSA:2.40.50.1070:FF:000004 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
11 66 Pfam PF01938 TRAM domain
11 66 InterPro IPR002792 TRAM domain
128 264 Gene3D G3DSA:2.40.50.1070 -
14 431 PANTHER PTHR11061 RNA M5U METHYLTRANSFERASE
14 431 InterPro IPR010280 (Uracil-5)-methyltransferase family
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
10 68 ProSiteProfiles PS50926 TRAM domain profile.
10 68 InterPro IPR002792 TRAM domain
161 431 Pfam PF05958 tRNA (Uracil-5-)-methyltransferase
161 431 InterPro IPR010280 (Uracil-5)-methyltransferase family
414 424 ProSitePatterns PS01231 RNA methyltransferase trmA family signature 2.
414 424 InterPro IPR030391 RNA methyltransferase TrmA, conserved site
1 87 Gene3D G3DSA:2.40.50.140 -
1 87 InterPro IPR012340 Nucleic acid-binding, OB-fold
88 426 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
88 426 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
88 432 ProSiteProfiles PS51687 SAM-dependent methyltransferase RNA m(5)U-type domain profile.
88 432 InterPro IPR010280 (Uracil-5)-methyltransferase family
250 426 FunFam G3DSA:3.40.50.150:FF:000009 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
24 424 NCBIfam TIGR00479 23S rRNA (uracil-5-)-methyltransferase RlmD
6 87 FunFam G3DSA:2.40.50.140:FF:000097 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
2 66 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
2 66 InterPro IPR012340 Nucleic acid-binding, OB-fold
289 389 CDD cd02440 AdoMet_MTases
76 431 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
76 431 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.634
Likely same site as FPocket 6 2.0 Å 18 shared residues 90% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.471
Likely same site as FPocket 1 2.3 Å 8 shared residues 73% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.105
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.011
Show in viewer
Surrounding area

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1
0.677
Likely same site as P2Rank 2 2.3 Å 8 shared residues 73% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #6
0.47
Likely same site as P2Rank 1 2.0 Å 18 shared residues 90% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:389-389
UniProt: Binding site:162-162
UniProt: Binding site:265-265
UniProt: Binding site:294-294
UniProt: Binding site:299-299
UniProt: Binding site:315-315
UniProt: Binding site:342-342
UniProt: Binding site:363-363
UniProt: Binding site:81-81
UniProt: Binding site:87-87
UniProt: Binding site:90-90
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GWU7
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4387
ColabFold — — full sequence — Loaded

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
Chemistry signal

Only proposed virtual-screening candidates are available for this target.

Direct evidence 0 same-protein records
Transferred evidence 0 records from similar proteins
Structural ligands 0 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ZINC12501520 ZINC proposed compound Tanimoto 1.000 458.5 Da · LogP -0.88 · TPSA 123.5 Open detail ZINC
ZINC3874716 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC4283769 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC4521548 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC5178829 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

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

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GWU7

Pathways

BioCyc RXN-11601