Protein target profile

VK055_1174

pyrF

Genome: KpATCC43816 Gene: pyrF AIK79797.1 3D evidence: Experimental + ColabFold model Metabolism 1 reaction UniProt A0A0H3GNE4
Length 228
Pocket druggability 0.65
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 4 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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
No hit
Gut microbiome similarity
4.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
85.526 Higher values support similarity to known essential genes.
DEG E-value
2.71e-141 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.04 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.65
Structure 8CSO
Pocket Pocket 2
P2Rank 0.688
Structure 8CSO
Pocket Pocket 1
ColabFold model
FPocket 0.529 · Pocket 4
P2Rank 0.734 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 189 / 4744 genomes with a hit
Prevalence 4.0%

Cross-references

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

Structure

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Attractive metabolic target: catalyzes a consuming chokepoint reaction in Pyrimidine metabolism, no isoenzyme backup detected, no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Chokepoint gene
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MVALDYDNRDKALAFVDRIDPRDCRLKVGKEMFTLLGPQFVRDLHQRGFEVFLDLKFHDIPNTTARAVAAAAELGVWMVNVHASGGARMMTAAREALLPFGKDAPLLIAVTVLTSMESSDLQDLGITLSPADYAAKLAALTQRCGLDGVVCSAQEAVRFKHELGQAFKLVTPGIRPQGSDAGDQRRIMTPEQAQEAGVDYMVIGRPVTQSADPAATLRAINDSLRKGA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0004590 Catalysis of the reaction: H+ + orotidine 5'-phosphate = CO2 + UMP.
  • GO:0006207 The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
  • GO:0044205 The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD+ or oxygen.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
2 220 Pfam PF00215 Orotidine 5'-phosphate decarboxylase / HUMPS family
2 220 InterPro IPR001754 Orotidine 5'-phosphate decarboxylase domain
1 225 Hamap MF_01200_B Orotidine 5'-phosphate decarboxylase [pyrF].
1 225 InterPro IPR047596 Orotidine 5'-phosphate decarboxylase, bacterial
1 228 FunFam G3DSA:3.20.20.70:FF:000015 Orotidine 5'-phosphate decarboxylase
1 223 SUPERFAMILY SSF51366 Ribulose-phoshate binding barrel
1 223 InterPro IPR011060 Ribulose-phosphate binding barrel
1 220 CDD cd04725 OMP_decarboxylase_like
1 220 SMART SM00934 OMPdecase_2
1 220 InterPro IPR001754 Orotidine 5'-phosphate decarboxylase domain
2 223 PANTHER PTHR32119 OROTIDINE 5'-PHOSPHATE DECARBOXYLASE
2 223 InterPro IPR014732 Orotidine 5'-phosphate decarboxylase
51 64 ProSitePatterns PS00156 Orotidine 5'-phosphate decarboxylase active site.
51 64 InterPro IPR018089 Orotidine 5'-phosphate decarboxylase, active site
1 228 Gene3D G3DSA:3.20.20.70 Aldolase class I
1 228 InterPro IPR013785 Aldolase-type TIM barrel
2 220 NCBIfam TIGR01740 orotidine-5'-phosphate decarboxylase
2 220 InterPro IPR014732 Orotidine 5'-phosphate decarboxylase

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 #2
0.65
Likely same site as P2Rank 3 2.8 Å 7 shared residues 100% of smaller site
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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
0.688
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.013
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Surrounding area
Site 3 P2Rank #3
0.007
Likely same site as FPocket 2 2.8 Å 7 shared residues 100% of smaller site
Show in viewer
Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

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
PDB 8CSO
X-ray 2.60 Å A,B,C,D,E,F,G,H,I,J
99.6% 2-228
Viewing
ColabFold VK055_1174
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
BMP PDB via homolog 340.2 Da · LogP -3.03 · TPSA 191.5 Open detail RCSB PDB
BMQ PDB via homolog Detail RCSB PDB
XPE PDB via homolog Detail RCSB PDB
ZINC12501520 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC3870485 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
BMP RCSB PDB P08244 340.2 Da LogP -3.03 TPSA 191.5 1 viol. ✓ Clean C1=C(N(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
BMQ RCSB PDB P08244 340.2 Da LogP -2.99 TPSA 182.9 ✓ Ro5 ✓ Clean C1C(=O)NC(=O)N(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O…
XPE RCSB PDB Q9KQT7 458.5 Da LogP -0.88 TPSA 123.5 1 viol. ✓ Clean C(COCCOCCOCCOCCOCCOCCOCCOCCOCCO)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.