Protein target profile

VK055_4003

urease, alpha subunit

Genome: KpATCC43816 Gene: AIK82550.1 ureC 3D evidence: Experimental + ColabFold model Metabolism 2 reactions UniProt A0A060VJP5
Length 567
Pocket druggability 0.672
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 59 total records
Functional annotation 1 EC 7 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
No hit
Gut microbiome similarity
7.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
62.61 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
98.16 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 0.672
Structure 8HCN
Pocket Pocket 5
P2Rank 0.619
Structure 8HCN
Pocket Pocket 1
ColabFold model
FPocket 0.687 · Pocket 1
P2Rank 0.117 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 352 / 4744 genomes with a hit
Prevalence 7.4%

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

Metabolic context: more central than 90.4% of genes in this genome, no human homolog detected.

Relative network centrality 90.4% more central than 90.4% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

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.

MSNISRQAYADMFGPTVGDKVRLADTELWIEVEDDLTTYGEEVKFGGGKVIRDGMGQGQMLAADCVDLVLTNALIVDHWGIVKADIGVKDGRIFAIGKAGNPDIQPNVTIPIGAATEVIAAEGKIVTAGGIDTHIHWICPQQAEEALVSGVTTMVGGGTGPAAGTHATTCTPGPWYISRMLQAADSLPVNIGLLGKGNVSQPDALREQVAAGVIGLKIHEDWGATPAAIDCALTVADEMDVQVALHSDTLNESGFVEDTLAAIGGRTIHTFHTEGAGGGHAPDIITACAHPNILPSSTNPTLPYTLNTIDEHLDMLMVCHHLDPDIAEDVAFAESRIRRETIAAEDVLHDLGAFSLTSSDSQAMGRVGEVILRTWQVAHRMKVQRGALAEETGDNDNFRVKRYIAKYTINPALTHGIAHEVGSIEVGKLADLVVWSPAFFGVKPATVIKGGMIAIAPMGDINASIPTPQPVHYRPMFGALGSARHHCRLTFLSQAAAANGVAERLNLRSAIAVVKGCRTVQKADMVHNSLQPNITVDAQTYEVRVDGELITSEPADVLPMAQRYFLF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0016810 Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
  • GO:0009039 Catalysis of the reaction: urea + 2 H2O + H+ = hydrogencarbonate + 2 NH4+.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0016151 Binding to a nickel (Ni) cation.
  • GO:0006807 OBSOLETE. The chemical reactions and pathways involving organic or inorganic compounds that contain nitrogen.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0043419 The chemical reactions and pathways resulting in the breakdown of urea, the water soluble compound O=C-(NH2)2.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

34 records
Show feature table
Start End DB Term Name
130 567 SUPERFAMILY SSF51556 Metallo-dependent hydrolases
130 567 InterPro IPR032466 Metal-dependent hydrolase
3 567 PANTHER PTHR43440 UREASE
2 177 SUPERFAMILY SSF51338 Composite domain of metallo-dependent hydrolases
2 177 InterPro IPR011059 Metal-dependent hydrolase, composite domain superfamily
3 566 CDD cd00375 Urease_alpha
3 566 InterPro IPR005848 Urease, alpha subunit
4 480 Gene3D G3DSA:2.30.40.10 Urease, subunit C, domain 1
4 480 InterPro IPR011059 Metal-dependent hydrolase, composite domain superfamily
334 350 PRINTS PR01752 Urea amidohydrolase (urease) protein signature
334 350 InterPro IPR005848 Urease, alpha subunit
427 440 PRINTS PR01752 Urea amidohydrolase (urease) protein signature
427 440 InterPro IPR005848 Urease, alpha subunit
401 416 PRINTS PR01752 Urea amidohydrolase (urease) protein signature
401 416 InterPro IPR005848 Urease, alpha subunit
295 312 PRINTS PR01752 Urea amidohydrolase (urease) protein signature
295 312 InterPro IPR005848 Urease, alpha subunit
422 477 SUPERFAMILY SSF51338 Composite domain of metallo-dependent hydrolases
422 477 InterPro IPR011059 Metal-dependent hydrolase, composite domain superfamily
4 567 NCBIfam TIGR01792 urease subunit alpha
4 567 InterPro IPR005848 Urease, alpha subunit
317 333 ProSitePatterns PS00145 Urease active site.
317 333 InterPro IPR017950 Urease active site
2 567 Hamap MF_01953 Urease subunit alpha [ureC].
2 567 InterPro IPR005848 Urease, alpha subunit
125 453 Pfam PF01979 Amidohydrolase family
125 453 InterPro IPR006680 Amidohydrolase-related
129 567 Gene3D G3DSA:3.20.20.140 -
129 567 ProSiteProfiles PS51368 Urease domain profile.
129 567 InterPro IPR017951 Urease alpha subunit, C-terminal
3 119 Pfam PF00449 Urease alpha-subunit, N-terminal domain
3 119 InterPro IPR011612 Urease alpha-subunit, N-terminal domain
127 140 ProSitePatterns PS01120 Urease nickel ligands signature.
127 140 InterPro IPR029754 Urease nickel binding site

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 #5
0.672
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #10
0.601
Likely same site as P2Rank 2 1.7 Å 9 shared residues 100% of smaller site
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Surrounding area
Site 3 FPocket #2
0.454
Likely same site as P2Rank 1 3.5 Å 15 shared residues 75% of smaller site
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Surrounding area
Site 4 FPocket #20
0.313
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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
0.619
Likely same site as FPocket 2 3.5 Å 15 shared residues 75% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.085
Likely same site as FPocket 10 1.7 Å 9 shared residues 100% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.034
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Surrounding area
Site 4 P2Rank #4
0.028
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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 8HCN
X-ray C Viewing
ColabFold VK055_4003
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.

59 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 9 records from similar proteins
Structural ligands 9 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2PA PDB via homolog 96.0 Da · LogP -1.00 · TPSA 89.3 Open detail RCSB PDB
9XN PDB via homolog Detail RCSB PDB
BO3 PDB via homolog Detail RCSB PDB
CO2 PDB via homolog Detail RCSB PDB
DBX 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
2PA RCSB PDB P41020 96.0 Da LogP -1.00 TPSA 89.3 ✓ Ro5 ✓ Clean NP(=O)(N)O
9XN RCSB PDB P41020 113.1 Da LogP -0.85 TPSA 66.5 ✓ Ro5 ✓ Clean NP(=S)(O)O
BO3 RCSB PDB P41020 61.8 Da LogP -2.05 TPSA 60.7 ✓ Ro5 ✓ Clean B(O)(O)O
CO2 RCSB PDB P18314 44.0 Da LogP -0.58 TPSA 34.1 ✓ Ro5 ✓ Clean C(=O)=O
DBX RCSB PDB P41020 190.2 Da LogP 0.34 TPSA 94.8 ✓ Ro5 ✓ Clean c1cc(c(cc1O)S(=O)(=O)O)O
DJM RCSB PDB P69996 277.3 Da LogP 2.09 TPSA 67.2 ✓ Ro5 ✓ Clean Cc1cc(cc(c1)n2ccnc2SCC(=O)NO)C
FLC RCSB PDB P41020 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
HAE RCSB PDB P18314 75.1 Da LogP -0.49 TPSA 49.3 ✓ Ro5 ✓ Clean CC(=O)NO
HQE RCSB PDB P41020 110.1 Da LogP 1.10 TPSA 40.5 ✓ Ro5 ✓ Clean c1cc(ccc1O)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.