Protein target profile

KP13_03141

Uridine kinase

Genome: KpKP13 Gene: AHE43644.1 udk 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVV7
Length 213
Pocket druggability 0.556
Direct ligand evidence 0 64 total records
Functional annotation 1 EC 8 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing 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 (%)
37.624 Lower values reduce human off-target concern.
Human E-value
2.91e-42
Gut microbiome similarity
7.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
68.159 Higher values support similarity to known essential genes.
DEG E-value
6.6999999999999994e-105 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.52 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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.

FPocket 0.556
Structure A0A0H3GVV7
Pocket Pocket 1
P2Rank 0.874
Structure A0A0H3GVV7
Pocket Pocket 1
ColabFold model
FPocket 0.696 · Pocket 1
P2Rank 0.872 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 370 / 4744 genomes with a hit
Prevalence 7.8%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MTDMSHQCVIVGIAGASASGKSLIASTLYRELREQVGDEHIGVIPEDSYYKDQSHLSMEERVKTNYDHPSSMDHSLLFQHLQMLKSGQPIELPVYSYVEHTRTPNTIHVEPKKVIILEGILLLTDARLRNELNFSIFVDTPLDICLMRRIKRDVNERGRSMDSVMAQYQKTVRPMFLQFIEPSKQYADIIVPRGGKNRIAIDILKAKISQFFE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0016773 Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
  • GO:0004849 Catalysis of the reaction: ATP + uridine = ADP + UMP.
  • GO:0016301 Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0043771 Catalysis of the reaction: ATP + cytidine = ADP + CMP.
  • GO:0044211 Any process which produces cytidine 5'-triphosphate (CTP) from derivatives of it, without de novo synthesis.
  • GO:0044206 Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
10 208 CDD cd02023 UMPK
10 208 InterPro IPR000764 Uridine kinase-like
21 213 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
16 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
5 213 Hamap MF_00551 Uridine kinase [udk].
5 213 InterPro IPR026008 Uridine kinase
1 7 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
5 213 Gene3D G3DSA:3.40.50.300 -
5 213 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
7 213 FunFam G3DSA:3.40.50.300:FF:000252 Uridine kinase
10 199 Pfam PF00485 Phosphoribulokinase / Uridine kinase family
10 199 InterPro IPR006083 Phosphoribulokinase/uridine kinase
8 205 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
8 205 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
8 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
6 213 NCBIfam TIGR00235 uridine kinase
6 213 InterPro IPR000764 Uridine kinase-like
9 190 PANTHER PTHR10285 URIDINE KINASE
157 168 PRINTS PR00988 Uridine kinase signature
8 25 PRINTS PR00988 Uridine kinase signature
87 102 PRINTS PR00988 Uridine kinase signature
143 153 PRINTS PR00988 Uridine kinase signature
179 192 PRINTS PR00988 Uridine kinase signature
42 53 PRINTS PR00988 Uridine kinase signature

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 · FPocket

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

Site 1 FPocket #1
0.556
Likely same site as P2Rank 1 3.9 Å 16 shared residues 100% of smaller site
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Surrounding area
Site 2 FPocket #3
0.484
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Surrounding area
Site 3 FPocket #6
0.455
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.874
Likely same site as FPocket 1 3.9 Å 16 shared residues 100% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.032
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Surrounding area
Site 3 P2Rank #3
0.019
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Surrounding area
Residue sets
UniProt: Binding site:15-22
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_A0A0H3GVV7
AlphaFold DB full sequence Viewing
ColabFold KP13_03141
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.

64 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 14 records from similar proteins
Structural ligands 12 0 loaded crystals
Measured bioactivity 2 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0JR PDB via homolog 309.4 Da · LogP -0.42 · TPSA 111.6 Open detail RCSB PDB
ACP PDB via homolog Detail RCSB PDB
CTN PDB via homolog Detail RCSB PDB
DTT PDB via homolog Detail RCSB PDB
G6P PDB via homolog 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
0JR RCSB PDB B5XYG3 309.4 Da LogP -0.42 TPSA 111.6 ✓ Ro5 ✓ Clean CC(C)(CO)[C@H](C(=O)NCCC(=O)NCc1cccnc1)O
ACP RCSB PDB Q5SKR5 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
CTN RCSB PDB Q5SKR5 243.2 Da LogP -2.56 TPSA 130.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
DTT RCSB PDB Q31PL2 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
G6P RCSB PDB Q31PL2 260.1 Da LogP -3.10 TPSA 156.9 1 viol. ✓ Clean C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)O)O)O)O)OP…
KEA RCSB PDB Q9BZX2 348.2 Da LogP -1.13 TPSA 205.9 ✓ Ro5 Alert C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
OS RCSB PDB A0A0H3K6J7 190.2 Da LogP -0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Os+3]
P6D RCSB PDB Q9BZX2 C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
PN4 RCSB PDB B5XYG3 288.4 Da LogP 0.18 TPSA 98.7 ✓ Ro5 ✓ Clean CCCCCNC(=O)CCNC(=O)[C@@H](C(C)(C)CO)O
SH2 RCSB PDB B5XYG3 366.4 Da LogP -0.04 TPSA 117.1 ✓ Ro5 ✓ Clean CC(C)(CO)[C@H](C(=O)NCCC(=O)NCCc1ccc2c(c1)OCO2)O
UZ0 RCSB PDB Q9BZX2 269.2 Da LogP -1.53 TPSA 153.3 ✓ Ro5 Alert C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
UZR RCSB PDB Q9BZX2 350.2 Da LogP -2.18 TPSA 201.4 ✓ Ro5 Alert C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…

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.