Protein profile
VK055_4597
RNA 2'-O ribose methyltransferase substrate binding family protein
Genome: KpATCC43816
Overview
Basic information about this protein and its source genome.
- Accession
- VK055_4597
- Gene
- AIK83131.1
- Status
- annotated
- Amino acids
- 361
- Structure source
- AlphaFold + ColabFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 31.944
- Human E-value
- 1.17e-09
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- DEG identity (%)
- 78.947
- DEG E-value
- 0.0
- Localization
- Cytoplasmic
- ColabFold pLDDT
- 75.89
Selected Druggability evidence
AlphaFold / UniProt modelSelected 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.
Sequence
Primary amino-acid sequence viewer.
Functional Annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Gene Ontology (GO)
6- GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
- GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
- GO:0003723 Binding to an RNA molecule or a portion thereof.
- GO:0008173 Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
- GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
- GO:0032259 The process in which a methyl group is covalently attached to a molecule.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 113 | 360 | PANTHER | PTHR46429 | 23S RRNA (GUANOSINE-2'-O-)-METHYLTRANSFERASE RLMB |
| 113 | 360 | InterPro | IPR004441 | RNA methyltransferase TrmH |
| 1 | 31 | MobiDBLite | mobidb-lite | consensus disorder prediction |
| 93 | 113 | MobiDBLite | mobidb-lite | consensus disorder prediction |
| 126 | 196 | Pfam | PF08032 | RNA 2'-O ribose methyltransferase substrate binding |
| 126 | 196 | InterPro | IPR013123 | RNA 2-O ribose methyltransferase, substrate binding |
| 38 | 85 | MobiDBLite | mobidb-lite | consensus disorder prediction |
| 125 | 200 | SMART | SM00967 | SpoU_sub_bind_2 |
| 125 | 200 | InterPro | IPR013123 | RNA 2-O ribose methyltransferase, substrate binding |
| 215 | 352 | Pfam | PF00588 | SpoU rRNA Methylase family |
| 215 | 352 | InterPro | IPR001537 | tRNA/rRNA methyltransferase, SpoU type |
| 195 | 361 | Gene3D | G3DSA:3.40.1280.10 | - |
| 195 | 361 | InterPro | IPR029026 | tRNA (guanine-N1-)-methyltransferase, N-terminal |
| 205 | 359 | SUPERFAMILY | SSF75217 | alpha/beta knot |
| 205 | 359 | InterPro | IPR029028 | Alpha/beta knot methyltransferases |
| 119 | 195 | SUPERFAMILY | SSF55315 | L30e-like |
| 119 | 195 | InterPro | IPR029064 | 50S ribosomal protein L30e-like |
| 114 | 194 | Gene3D | G3DSA:3.30.1330.30 | - |
| 114 | 194 | InterPro | IPR029064 | 50S ribosomal protein L30e-like |
| 1 | 113 | MobiDBLite | mobidb-lite | consensus disorder prediction |
| 1 | 361 | PIRSF | PIRSF006280 | YfiF |
| 1 | 361 | InterPro | IPR016479 | tRNA/rRNA methyltransferase, YfiF, predicted |
| 214 | 355 | CDD | cd18095 | SpoU-like_rRNA-MTase |
| 114 | 194 | FunFam | G3DSA:3.30.1330.30:FF:000010 | tRNA/rRNA methyltransferase |
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...
Structural evidence
0 + 2Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.
| Entry | Method | Resolution | Chain | Coverage | Links | Status |
|---|---|---|---|---|---|---|
|
AlphaFold
AF_A0A0H3H1M1
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_4597
|
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 |
|---|---|---|---|---|---|---|---|
| 24 | 0.284 | ||||||
| 2 | 0.065 | ||||||
| 13 | 0.016 | ||||||
| 11 | 0.002 |
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 | Sticks | Spheres | Surfaces | Score | Probability | Labels | Zoom | Positions |
|---|---|---|---|---|---|---|---|---|
| 1 | 8.6 | 0.392 | ||||||
| 2 | 3.89 | 0.124 | ||||||
| 3 | 3.35 | 0.094 | ||||||
| 4 | 0.92 | 0.004 | ||||||
| 5 | 0.53 | 0.0 |
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 |
|---|---|---|---|---|---|---|---|
| 10 | 0.359 | ||||||
| 18 | 0.072 | ||||||
| 2 | 0.001 | ||||||
| 13 | 0.0 |
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 | Sticks | Spheres | Surfaces | Score | Probability | Labels | Zoom | Positions |
|---|---|---|---|---|---|---|---|---|
| 1 | 8.47 | 0.385 | ||||||
| 2 | 0.78 | 0.002 |
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.
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).
| Ligand | UniProt (homolog) | pchembl | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| DWT | Q6IN84 | 7.25 | 503.5 Da LogP 5.75 TPSA 97.6 | 2 viol. | ✓ Clean |
Cc1ccc(cc1Nc2c3cn(nc3nc(n2)c4cccnc4)C)C(=O)Nc5c…
|
| CHEMBL4129274 | Q13395 | — | 851.5 Da LogP 4.76 TPSA 183.3 | 3 viol. | Alert |
C=CC(=O)Nc1ccccc1Nc1nc(Nc2ccc(N3CCN(CCOCCOCCOCC…
|
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 |
|---|---|---|---|---|---|
| ZINC71842002 | 0.552 | 445.6 Da LogP 2.04 TPSA 76.7 | ✓ Ro5 | ✓ Clean |
O=C(CCCC[C@@H]1SC[C@@H]2NC(=O)N[C@H]12)NCCCN1CC…
|
| ZINC220133900 | 0.538 | 398.3 Da LogP 3.77 TPSA 85.1 | ✓ Ro5 | ✓ Clean |
Cc1nc2nc(-c3cccnc3)nn2cc1C(=O)Nc1cccc(C(F)(F)F)…
|
| ZINC20148987 | 0.532 | 414.4 Da LogP 4.50 TPSA 97.1 | ✓ Ro5 | ✓ Clean |
Cc1ccc(C(=O)Nc2cccc(C(F)(F)F)c2)cc1Nc1cncc(C(N)…
|
| ZINC914431236 | 0.531 | 464.0 Da LogP 4.49 TPSA 85.4 | ✓ Ro5 | Alert |
C=CC(=O)Nc1ccccc1Nc1nc(Nc2ccc(N3CCN(C)CC3)cc2)n…
|
| ZINC9306398 | 0.512 | 398.3 Da LogP 3.77 TPSA 85.1 | ✓ Ro5 | ✓ Clean |
Cc1c(C(=O)Nc2cccc(C(F)(F)F)c2)cnc2nc(-c3cccnc3)…
|
| ZINC5049572 | 0.507 | 336.3 Da LogP 4.22 TPSA 58.2 | ✓ Ro5 | ✓ Clean |
CC(=O)Nc1cc(C(=O)Nc2cccc(C(F)(F)F)c2)ccc1C
|
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.