KpKP13 Protein target profile

Ribosomal large subunit pseudouridine synthase D

Accession: KP13_31626

Gene: AHE43153.1 rluD 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GRV8
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Length 326
Pocket druggability (P2Rank · AlphaFold DB model) 0.231
Direct ligand evidence 0 1 total records
Functional annotation 0 EC 4 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Moderate predicted binding pocket FPocket selected-pocket score 0.43. This supports review but is not experimental validation. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 1 structural and 0 bioactivity records.

Risks to review

Human similarity Top human hit identity: 43.396%. This target also has a predicted binding pocket (P2Rank 0.23) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 191 of 4744 screened genomes (4.0%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.23) — check the ligand evidence before deprioritizing on off-target risk alone. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.23.

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 (%)
43.396 Lower values reduce human off-target concern.
Human E-value
3.94e-06
Gut microbiome similarity
4.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
92.025 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
92.93 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) 0.231
Structure A0A0H3GRV8
Pocket Pocket 1
Druggability (FPocket) 0.433
Structure A0A0H3GRV8
Pocket Pocket 18
ColabFold model
P2Rank 0.153 · Pocket 1
FPocket 0.39 · Pocket 21
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 191 / 4744 genomes with a hit
Prevalence 4.0%

Sequence

Primary amino-acid sequence viewer.

MAQRVQLTATVTENQLGQRLDQALAELFPDYSRSRIKEWILDQRVLVNGTIGDKPKEKVLGGERIAIDVEIEEEARFQPQDIPLNIVYEDDDIIVINKPRDLVVHPGAGNPDGTVLNALLHYYPPIADVPRAGIVHRLDKDTTGLMVVAKTIPAQTRLVESLQLREITREYEAVAIGHMTAGGTVEEPISRHPTKRTHMAVHPMGKPAVTHYRIMEHFRIHTRLRLRLETGRTHQIRVHMSHITHPLVGDQVYGGRPRPPKGASEEFITALRKFDRQALHATMLRLYHPISGIEMEWHAPIPQDMVELIEAMRADFEAHKDDIDWL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Subcellular localization

Localization
Cytoplasmic

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 domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
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; 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
0.231
Likely same site as FPocket 18 4.9 Å 12 shared residues 92% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.119
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Surrounding area
Pocket 3 P2Rank #3
0.094
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Surrounding area
Pocket 4 P2Rank #4
0.043
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Surrounding area
Pocket 5 P2Rank #5
0.01
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #18
0.433
Likely same site as P2Rank 1 4.9 Å 12 shared residues 92% of smaller site
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Surrounding area
Pocket 2 FPocket #17
0.32
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Surrounding area
Residue sets
UniProt: Active site:113-113
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_A0A0H3GRV8
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_31626
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.

1 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 0 similarity-based ZINC candidates
Best available ligand signal
FOU PDB via homolog 150.1 Da · LogP -1.73 · TPSA 81.6 Open detail RCSB PDB

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
FOU RCSB PDB
2I82
P0AA37 150.1 Da LogP -1.73 TPSA 81.6 ✓ Ro5 ✓ Clean [C@H]1(C([C@H](NC(=O)N1)O)F)O

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 A0A0H3GRV8