Protein target profile
PA0933
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
Genome: NC_002516.2
Target candidate with partial support; inspect missing evidence before prioritizing.
2 signalsStrengths
Risks / watch
How to read 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 TPW 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.
Overview
Basic information about this protein and its source genome.
- Accession
- PA0933
- Gene
- ygcA
- Status
- annotated
- Amino acids
- 450
- 3D evidence
- ColabFold model
Target profile
Computed evidence for target prioritization.
- Human off-target
- Hit
- Human identity (%)
- 38.021
- Human E-value
- 1.04e-22
- Gut microbiome off-target
- Hit
- Essential (DEG)
- N
- Localization
- Cytoplasmic
Selected pocket evidence
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.
Sequence
Primary amino-acid sequence viewer.
MARNKGGLRFQPSGGARGPAIPVGKKQRLTIERLAHDGRGIAHEAGMTWFVSGGLPGEELEARVLGARSKVVDARSERLFSSSDLRRREPCTVAGRCGGCTLQHLEHGEQLALKQRTLQEQLQRFAGIEPEEWAAPLVGPEFGYRRRARIAVRWDARARRLDVGFRASASQEIVAFDECLVLVPPLQTIARALPALLQDFRKPESIGHVELFHGTASALLLRHTTALVDEDRQRLAAFCSAHQAQLWLQGAEQPLPVEPAAELGYSLGDWQLTLAYRPGDFVQVNAPVNESMIRQALDWLAPTADERVLDLFCGLGNFSLPLARRVARVVGVEGVAAMVERAGANALANGLGNAHFFQADLSKALAEAPWAEQGFTAVLLDPPRDGAFEAVREMSSLGARRVVYVSCNPATLARDAGEMARQGYRLKRAGILDMFPQTAHVEAMALFEAG
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
3- GO:0003723 Binding to an RNA molecule or a portion thereof.
- 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.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 98 | 444 | Gene3D | G3DSA:3.40.50.150 | Vaccinia Virus protein VP39 |
| 98 | 444 | InterPro | IPR029063 | S-adenosyl-L-methionine-dependent methyltransferase superfamily |
| 109 | 446 | Pfam | PF05958 | tRNA (Uracil-5-)-methyltransferase |
| 109 | 446 | InterPro | IPR010280 | (Uracil-5)-methyltransferase family |
| 145 | 282 | Gene3D | G3DSA:2.40.50.1070 | - |
| 271 | 448 | PANTHER | PTHR11061 | RNA M5U METHYLTRANSFERASE |
| 271 | 448 | InterPro | IPR010280 | (Uracil-5)-methyltransferase family |
| 19 | 97 | FunFam | G3DSA:2.40.50.140:FF:000458 | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD |
| 19 | 97 | Gene3D | G3DSA:2.40.50.140 | - |
| 19 | 97 | InterPro | IPR012340 | Nucleic acid-binding, OB-fold |
| 28 | 450 | Hamap | MF_01010 | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD [rlmD]. |
| 28 | 450 | InterPro | IPR001566 | 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD |
| 98 | 450 | ProSiteProfiles | PS51687 | SAM-dependent methyltransferase RNA m(5)U-type domain profile. |
| 98 | 450 | InterPro | IPR010280 | (Uracil-5)-methyltransferase family |
| 20 | 78 | ProSiteProfiles | PS50926 | TRAM domain profile. |
| 20 | 78 | InterPro | IPR002792 | TRAM domain |
| 272 | 442 | NCBIfam | TIGR00479 | 23S rRNA (uracil-5-)-methyltransferase RlmD |
| 307 | 394 | CDD | cd02440 | AdoMet_MTases |
| 1 | 21 | MobiDBLite | mobidb-lite | consensus disorder prediction |
| 270 | 444 | FunFam | G3DSA:3.40.50.150:FF:000009 | 23S rRNA (Uracil(1939)-C(5))-methyltransferase RlmD |
| 17 | 74 | SUPERFAMILY | SSF50249 | Nucleic acid-binding proteins |
| 17 | 74 | InterPro | IPR012340 | Nucleic acid-binding, OB-fold |
| 381 | 411 | ProSitePatterns | PS01230 | RNA methyltransferase trmA family signature 1. |
| 381 | 411 | InterPro | IPR030390 | RNA methyltransferase TrmA, active site |
| 432 | 442 | ProSitePatterns | PS01231 | RNA methyltransferase trmA family signature 2. |
| 432 | 442 | InterPro | IPR030391 | RNA methyltransferase TrmA, conserved site |
| 86 | 448 | SUPERFAMILY | SSF53335 | S-adenosyl-L-methionine-dependent methyltransferases |
| 86 | 448 | 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.
Loading 3D structure...
Structural evidence
0 + 1Experimental 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 |
|---|---|---|---|---|---|---|
|
ColabFold
PA0933
|
ColabFold | — | — | full sequence | — | Viewing |
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Inspect mode shows the specific pocket/cavity and hides other active pocket layers. Use Surface when you need the wider residue environment.
Binding pockets · FPocket
Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
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.
Only proposed virtual-screening candidates are available for this target.
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 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.