Protein profile
KP13_31626
Ribosomal large subunit pseudouridine synthase D
Genome: KpKP13
Overview
Basic information about this protein and its source genome.
- Accession
- KP13_31626
- Gene
- AHE43153.1 rluD
- Status
- annotated
- Amino acids
- 326
- Structure source
- AlphaFold + ColabFold
Target profile
Computed evidence for target prioritization.
- Human off-target
- hit
- Human identity (%)
- 43.396
- Human E-value
- 3.94e-06
- Gut microbiome off-target
- hit
- Essential (DEG)
- Y
- DEG identity (%)
- 92.025
- DEG E-value
- 0.0
- Localization
- Cytoplasmic
- ColabFold pLDDT
- 92.93
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)
4- GO:0003723 Binding to an RNA molecule or a portion thereof.
- GO:0001522 The intramolecular conversion of uridine to pseudouridine within an RNA molecule.
- GO:0009451 The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
- GO:0009982 Catalysis of the reaction: a uridine in RNA = a pseudouridine in RNA. Conversion of uridine in an RNA molecule to pseudouridine by rotation of the C1'-N-1 glycosidic bond of uridine in RNA to a C1'-C5.
Sequence Features
Domain/signature hits from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 84 | 298 | Gene3D | G3DSA:3.30.2350.10 | Pseudouridine synthase |
| 13 | 312 | PANTHER | PTHR21600 | MITOCHONDRIAL RNA PSEUDOURIDINE SYNTHASE |
| 18 | 97 | CDD | cd00165 | S4 |
| 93 | 286 | CDD | cd02869 | PseudoU_synth_RluA_like |
| 93 | 286 | InterPro | IPR006145 | Pseudouridine synthase, RsuA/RluA-like |
| 2 | 76 | Gene3D | G3DSA:3.10.290.10 | - |
| 2 | 76 | InterPro | IPR036986 | RNA-binding S4 domain superfamily |
| 2 | 76 | FunFam | G3DSA:3.10.290.10:FF:000011 | Pseudouridine synthase |
| 17 | 70 | SUPERFAMILY | SSF55174 | Alpha-L RNA-binding motif |
| 84 | 298 | FunFam | G3DSA:3.30.2350.10:FF:000004 | Pseudouridine synthase |
| 18 | 65 | Pfam | PF01479 | S4 domain |
| 18 | 65 | InterPro | IPR002942 | RNA-binding S4 domain |
| 77 | 322 | SUPERFAMILY | SSF55120 | Pseudouridine synthase |
| 77 | 322 | InterPro | IPR020103 | Pseudouridine synthase, catalytic domain superfamily |
| 18 | 91 | ProSiteProfiles | PS50889 | S4 RNA-binding domain profile. |
| 13 | 313 | NCBIfam | TIGR00005 | RluA family pseudouridine synthase |
| 13 | 313 | InterPro | IPR006225 | Pseudouridine synthase, RluC/RluD |
| 92 | 242 | Pfam | PF00849 | RNA pseudouridylate synthase |
| 92 | 242 | InterPro | IPR006145 | Pseudouridine synthase, RsuA/RluA-like |
| 135 | 149 | ProSitePatterns | PS01129 | Rlu family of pseudouridine synthase signature. |
| 135 | 149 | InterPro | IPR006224 | Pseudouridine synthase, RluA-like, conserved site |
| 299 | 321 | Gene3D | G3DSA:6.10.140.230 | - |
| 18 | 79 | SMART | SM00363 | s4_6 |
| 18 | 79 | InterPro | IPR002942 | RNA-binding S4 domain |
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_A0A0H3GRV8
|
AlphaFold | — | — | full sequence | — | Viewing |
|
ColabFold
KP13_31626
|
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 |
|---|---|---|---|---|---|---|---|
| 18 | 0.433 | ||||||
| 17 | 0.32 |
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 | 5.0 | 0.227 | ||||||
| 2 | 1.73 | 0.031 | ||||||
| 3 | 1.72 | 0.03 | ||||||
| 4 | 0.99 | 0.005 |
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 |
|---|---|---|---|---|---|---|---|
| 21 | 0.39 | ||||||
| 12 | 0.241 | ||||||
| 14 | 0.203 |
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 | 1.62 | 0.026 | ||||||
| 2 | 1.48 | 0.021 |
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.
| Ligand | Source crystal | UniProt (homolog) | MW · LogP · TPSA | Lipinski | PAINS | SMILES |
|---|---|---|---|---|---|---|
| FOU | P0AA37 | 150.1 Da LogP -1.73 TPSA 81.6 | ✓ Ro5 | ✓ Clean |
[C@H]1(C([C@H](NC(=O)N1)O)F)O
|
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).
No virtual-screening candidates for this protein.
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.