Protein target profile

KP13_04249

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

Genome: KpKP13 Gene: AHE45481.1 rumB 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GKV4
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Length 347
Pocket druggability 0.94
Direct ligand evidence 0 50 total records
Functional annotation 1 EC 8 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

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.94, P2Rank 0.69). Use the 3D pocket comparison to verify whether they identify the same site. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.94. This is a computational pocket signal, not binding validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.69. Review the complete evidence below

Risks to review

Low human similarity A human hit was flagged, but identity is only 28.643% - a weak match, lower risk than a close homolog. This target also has a predicted binding pocket (FPocket 0.94) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 137 of 4744 screened genomes (2.9%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.94) — check the ligand evidence before deprioritizing on off-target risk alone. Only proposed compounds 50 ZINC similarity-based candidates, no stronger ligand evidence.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein.
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 (%)
28.643 Lower values reduce human off-target concern.
Human E-value
8.42e-17
Gut microbiome similarity
2.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.81 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.94
Structure A0A0H3GKV4
Pocket Pocket 19
P2Rank 0.685
Structure A0A0H3GKV4
Pocket Pocket 1
ColabFold model
FPocket 0.74 · Pocket 4
P2Rank 0.668 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 137 / 4744 genomes with a hit
Prevalence 2.9%

Cross-references

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

Sequence

UniProt A0A0H3GKV4

Sequence

Primary amino-acid sequence viewer.

MADLRTLLAAIPVAAWGEPVSGPEAAFRNKAKMVVSGSVERPLLGMLHRDGTPVDLTDCPLYPAEFATVFAALKPFIARAGLTPYNVARKRGELKYLLLTASQQGEMMLRFVLRSEAKVAQLRAALPWLQAQLPQLSVITANIQPVHMAIMEGEQEIFFTEQQALGEVFNGVPLWIRPQSFFQTNPAVASRLYATARDWVRALPVQHMWDLFCGVGGFGLHCATPTMRLTGIEIAPEAIACARQSAAQLGLSNLHFQALDSTQFATHEADAPQLVLVNPPRRGIGAELCDYLSRMAPPYIIYSSCNARTMATDIARLSGYRVERVQLFDMFPHTAHYEVLTLLVREV

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0008173 Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
  • GO:0016070 The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
  • GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
  • GO:0016436 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing methyluridine.
  • 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.

25 records
Show feature table
Start End DB Term Name
28 182 Gene3D G3DSA:2.40.50.1070 -
1 5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
18 345 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
18 345 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
28 182 FunFam G3DSA:2.40.50.1070:FF:000002 23S rRNA (uracil(747)-C(5))-methyltransferase RlmC
179 345 Pfam PF05958 tRNA (Uracil-5-)-methyltransferase
179 345 InterPro IPR010280 (Uracil-5)-methyltransferase family
209 280 CDD cd02440 AdoMet_MTases
278 309 ProSitePatterns PS01230 RNA methyltransferase trmA family signature 1.
278 309 InterPro IPR030390 RNA methyltransferase TrmA, active site
24 339 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
24 339 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
1 17 SignalP_EUK SignalP-noTM SignalP-noTM
2 345 NCBIfam TIGR02085 23S rRNA (uracil(747)-C(5))-methyltransferase
2 345 InterPro IPR011825 23S rRNA (uracil(747)-C(5))-methyltransferase RlmC
328 338 ProSitePatterns PS01231 RNA methyltransferase trmA family signature 2.
328 338 InterPro IPR030391 RNA methyltransferase TrmA, conserved site
1 346 ProSiteProfiles PS51687 SAM-dependent methyltransferase RNA m(5)U-type domain profile.
1 346 InterPro IPR010280 (Uracil-5)-methyltransferase family
24 343 PANTHER PTHR11061 RNA M5U METHYLTRANSFERASE
24 343 InterPro IPR010280 (Uracil-5)-methyltransferase family
18 347 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 17 Phobius SIGNAL_PEPTIDE Signal peptide region
14 17 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
6 13 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.

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 · FPocket

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

Site 1 FPocket #19
0.94
Likely same site as P2Rank 1 3.3 Å 18 shared residues 82% of smaller site
Unusual size
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Surrounding area
Site 2 FPocket #15
0.238
Likely same site as P2Rank 3 1.5 Å 11 shared residues 92% of smaller site
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Surrounding area
Site 3 FPocket #7
0.2
Likely same site as P2Rank 2 1.4 Å 14 shared residues 93% of smaller site
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.685
Likely same site as FPocket 19 3.3 Å 18 shared residues 82% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.647
Likely same site as FPocket 7 1.4 Å 14 shared residues 93% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.045
Likely same site as FPocket 15 1.5 Å 11 shared residues 92% of smaller site
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.017
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.006
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:333-333
UniProt: Binding site:11-11
UniProt: Binding site:14-14
UniProt: Binding site:211-211
UniProt: Binding site:240-240
UniProt: Binding site:261-261
UniProt: Binding site:3-3
UniProt: Binding site:306-306
UniProt: Binding site:87-87
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_A0A0H3GKV4
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_04249
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.