Protein target profile

VK055_3095

uroporphyrinogen decarboxylase

Genome: KpATCC43816 Gene: hemE AIK81676.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GQ14
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Length 354
Pocket druggability 0.095
Metabolic reactions 2
Chokepoint Yes
Direct ligand evidence 0 4 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.

Main supporting evidence

Metabolic bottleneck Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Central metabolic position More central than 96.2% of genes in this genome. No isoenzyme backup detected Imported GPR rules do not show an alternative enzyme for the catalyzed reaction set. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Review the complete evidence below

Risks to review

Human similarity Top human hit identity: 70.175%. Microbiome similarity 249 of 4744 screened genomes (5.2%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.10.

Evidence coverage

Core evidence streams are available for this target.
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 (%)
70.175 Lower values reduce human off-target concern.
Human E-value
4.41e-21
Gut microbiome similarity
5.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.64 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 0.095
Structure A0A0H3GQ14
Pocket Pocket 16
P2Rank 0.86
Structure A0A0H3GQ14
Pocket Pocket 1
ColabFold model
FPocket 0.08 · Pocket 15
P2Rank 0.871 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 249 / 4744 genomes with a hit
Prevalence 5.2%

Cross-references

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

Sequence

UniProt A0A0H3GQ14

Pathways

KEGG R03197 BioCyc UROGENDECARBOX-RXN KEGG R04972 BioCyc RXN-10642

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a producing chokepoint reaction in Porphyrin metabolism, no isoenzyme backup detected, more central than 96.2% of genes in this genome.

Relative network centrality 96.2% more central than 96.2% of genes in this genome
Chokepoint Chokepoint gene
Pathways
Porphyrin metabolism
Catalyzed reactions

2 reactions 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.

MTELKNDRYLRALLRQPVDVTPVWMMRQAGRYLPEYKATRAQAGDFMSLCKNAELACEVTLQPLRRYPLDAAILFSDILTIPDAMGLGLYFEAGEGPRFTSPVKSKADVDKLPIPDPEQELGYVMNAVRTIRRELKGEVPLIGFSGSPWTLATYMVEGGTSKAFTVIKKMMYAEPQALHALLDKLAKSVTLYLNAQIKAGAQSVMIFDTWGGVLTGRDYQQFSLYYMHKIVDGLLRENEGRRVPVTLFTKGGGQWLEAMAETGCDALGLDWTTDIADARRRVGNKVALQGNMDPSMLYASAPRIEEEVATILAGFGQGEGHVFNLGHGIHQDVDPEHAGVFVEAVHRLSAPYHQ

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:0004853 Catalysis of the reaction: uroporphyrinogen-III = coproporphyrinogen + 4 CO2.
  • GO:0006779 The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0019353 The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX from other compounds, including glutamate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
1 353 SUPERFAMILY SSF51726 UROD/MetE-like
1 353 InterPro IPR038071 UROD/MetE-like superfamily
6 349 Hamap MF_00218 Uroporphyrinogen decarboxylase [hemE].
6 349 InterPro IPR006361 Uroporphyrinogen decarboxylase HemE
10 347 CDD cd00717 URO-D
10 347 InterPro IPR006361 Uroporphyrinogen decarboxylase HemE
1 353 Gene3D G3DSA:3.20.20.210 -
3 350 PANTHER PTHR21091 METHYLTETRAHYDROFOLATE:HOMOCYSTEINE METHYLTRANSFERASE RELATED
5 347 Pfam PF01208 Uroporphyrinogen decarboxylase (URO-D)
5 347 InterPro IPR000257 Uroporphyrinogen decarboxylase (URO-D)
142 158 ProSitePatterns PS00907 Uroporphyrinogen decarboxylase signature 2.
142 158 InterPro IPR000257 Uroporphyrinogen decarboxylase (URO-D)
1 353 FunFam G3DSA:3.20.20.210:FF:000001 Uroporphyrinogen decarboxylase
22 31 ProSitePatterns PS00906 Uroporphyrinogen decarboxylase signature 1.
22 31 InterPro IPR000257 Uroporphyrinogen decarboxylase (URO-D)
9 347 NCBIfam TIGR01464 uroporphyrinogen decarboxylase
9 347 InterPro IPR006361 Uroporphyrinogen decarboxylase HemE

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

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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

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

Site 1 P2Rank #1
0.86
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:154-154
UniProt: Binding site:209-209
UniProt: Binding site:27-31
UniProt: Binding site:327-327
UniProt: Binding site:77-77
UniProt: Site:77-77 Transition state stabilizer
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_A0A0H3GQ14
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_3095
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.

4 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 1 similarity-based ZINC candidates
Best available ligand signal
1CP PDB via homolog 660.8 Da · LogP 4.98 · TPSA 212.4 Open detail RCSB PDB
CO2 PDB via homolog Detail RCSB PDB
CP3 PDB via homolog Detail RCSB PDB
ZINC4202772 ZINC proposed compound · Tanimoto 0.514 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
1CP RCSB PDB
1R3S
P06132 660.8 Da LogP 4.98 TPSA 212.4 2 viol. ✓ Clean Cc1c2[nH]c(c1CCC(=O)O)Cc3c(c(c([nH]3)Cc4c(c(c([…
CO2 RCSB PDB
1R3Q
P06132 44.0 Da LogP -0.58 TPSA 34.1 ✓ Ro5 ✓ Clean C(=O)=O
CP3 RCSB PDB
1R3T
P06132 660.8 Da LogP 4.98 TPSA 212.4 2 viol. ✓ Clean Cc1c2[nH]c(c1CCC(=O)O)Cc3c(c(c([nH]3)Cc4c(c(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.