KpKP13 Protein target profile

tRNA-dihydrouridine synthase A

Accession: KP13_08655

Gene: ANJ86641.1 dusA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GKY9

Export view

Length 331

Pocket druggability (P2Rank · AlphaFold DB model) 0.945

Functional annotation 1 EC 8 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

Moderate predicted binding pocket FPocket selected-pocket score 0.42. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.94. Structure available AlphaFold DB model + ColabFold model

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for this protein. No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.

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 (%): 32.099 Lower values reduce human off-target concern.
Human E-value: 5.81e-08
Gut microbiome similarity: 5.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 67.89 Higher values support similarity to known essential genes.
DEG E-value: 6.61e-165 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 94.5 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) 0.945

Structure A0A0H3GKY9

Pocket Pocket 1

Druggability (FPocket) 0.416

Structure A0A0H3GKY9

Pocket Pocket 10

ColabFold model

P2Rank 0.94 · Pocket 1

FPocket 0.364 · Pocket 5

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 271 / 4744 genomes with a hit

Prevalence 5.7%

Sequence

Primary amino-acid sequence viewer.

MPESTSPVFPAHRFSIAPMLDWTDRHCRYFLRLLSRHTLLYTEMVTTGAIIHGKGDYLAYSEEEHPVALQLGGSDPQALAQCAKLAEARGYDEINLNVGCPSDRVQNGMFGACLMGNAPLVADCIKAMRDVVSIPVTVKTRIGIDDQDSYEFLCDFIETVSGKGECEMFIIHARKAWLSGLSPKENREIPPLDYPRVWQLKRDFPHLTMAINGGIKSLDEARAQLEHMDGVMVGREAYQNPGILASVDREIFGVAGADADPVAVVRAMYPYIERELSKGTYLGHITRHMLGLFQGIPGARQWRRYLSENAHKAGADIAVLEHALKLVADKR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

1.3.1.91

Gene Ontology (GO)

GO:0017150 Catalysis of the reaction: a 5,6-dihydrouridine in tRNA + NAD(P)+ = a uridine in tRNA + H+ + NAD(P)H.
GO:0002943 The process whereby a uridine in a transfer RNA is converted to dihydrouridine.
GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
GO:0050660 Binding to FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
GO:0010181 Binding to flavin mono nucleotide. Flavin mono nucleotide (FMN) is the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
GO:0000049 Binding to a transfer RNA.
GO:0102264 Catalysis of the reaction: a 5,6-dihydrouracil20 in tRNA + NAD(P) = H+ + a uracil20 in tRNA + NAD(P)H.
GO:0102266 Catalysis of the reaction: a 5,6-dihydrouracil20a in tRNA + NAD(P) = H+ + a uracil20a in tRNA + NAD(P)H.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
258	330	Gene3D	G3DSA:1.20.120.1460	-
13	252	CDD	cd02801	DUS_like_FMN
13	252	InterPro	IPR035587	DUS-like, FMN-binding domain
257	330	FunFam	G3DSA:1.20.120.1460:FF:000001	tRNA-dihydrouridine(20/20a) synthase
3	326	PIRSF	PIRSF006621	Dus
3	326	InterPro	IPR001269	tRNA-dihydrouridine synthase
13	328	NCBIfam	TIGR00742	tRNA dihydrouridine(20/20a) synthase DusA
13	328	InterPro	IPR004653	tRNA-dihydrouridine(20/20a) synthase
12	313	SUPERFAMILY	SSF51395	FMN-linked oxidoreductases
8	329	Hamap	MF_02041	tRNA-dihydrouridine(20/20a) synthase [dusA].
8	329	InterPro	IPR004653	tRNA-dihydrouridine(20/20a) synthase
11	330	PANTHER	PTHR42907	FMN-LINKED OXIDOREDUCTASES SUPERFAMILY PROTEIN
11	330	InterPro	IPR004653	tRNA-dihydrouridine(20/20a) synthase
11	252	FunFam	G3DSA:3.20.20.70:FF:000083	tRNA-dihydrouridine(20/20a) synthase
94	112	ProSitePatterns	PS01136	Uncharacterized protein family UPF0034 signature.
94	112	InterPro	IPR018517	tRNA-dihydrouridine synthase, conserved site
11	252	Gene3D	G3DSA:3.20.20.70	Aldolase class I
11	252	InterPro	IPR013785	Aldolase-type TIM barrel
16	325	Pfam	PF01207	Dihydrouridine synthase (Dus)
16	325	InterPro	IPR035587	DUS-like, FMN-binding 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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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

0.945

Likely same site as FPocket 10 1.8 Å 29 shared residues 94% of smaller site

Show in viewer

Surrounding area

Pocket 2 P2Rank #2

0.016

Show in viewer

Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #10

0.416 Unusual size

Likely same site as P2Rank 1 1.8 Å 29 shared residues 94% of smaller site

Show in viewer

Surrounding area

Residue sets

UniProt: Active site:101-101 Proton donor

UniProt: Binding site:140-140

UniProt: Binding site:173-173

UniProt: Binding site:19-21

UniProt: Binding site:213-215

UniProt: Binding site:235-236

UniProt: Binding site:71-71

UniProt: Site:185-185 Interacts with tRNA; defines subfamily-specific binding signature

UniProt: Site:188-188 Interacts with tRNA

UniProt: Site:301-301 Interacts with tRNA; defines subfamily-specific binding signature

UniProt: Site:304-304 Interacts with tRNA; defines subfamily-specific binding signature

UniProt: Site:98-98 Interacts with tRNA

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_A0A0H3GKY9	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_08655	ColabFold	—	—	full sequence	—	Loaded

Cross-references

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

Sequence

UniProt A0A0H3GKY9