KpATCC43816 Protein target profile

urease, alpha subunit

Accession: VK055_4194

Gene: ureC2 AIK82739.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A2L1BU89
Length 572
Pocket druggability (P2Rank · AlphaFold DB model) 0.146
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 (%)
55.185 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.8 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) 0.146
Structure A0A2L1BU89
Pocket Pocket 1
Druggability (FPocket) 0.831
Structure A0A2L1BU89
Pocket Pocket 20
ColabFold model
P2Rank 0.18 · Pocket 1
FPocket 0.932 · Pocket 7
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 352 / 4744 genomes with a hit
Prevalence 7.4%

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.

MPTISRKEYASLFGPTVGDKIRLGETDLYIEIEKDLRGYGDESVYGGGKSLRDGMGSNNTLTRDNGVLDLVITNVTILDAKLGVIKADVGIKDGLIVGIGKSGNPAIMDGVTQNMIVGLSTDAISGEHLILTAAGIDSHIHLISPQQAYSALSNGVATFFGGGIGPTDGTNGTTVTPGPWNIGKMLRAVEGLPVNVGLLGKGNAFGRAPLVEQIIAGVAGLKVHEDWGATPNALRHSLRIADEMDIQVSVHTDSLNEAGYVENTIEAFEGRTIHTFHTEGAGGGHAPDIIKVASQLNVLPSSTNPTLPFGINTQAELFDMIMVCHNLNPNVAADVSFAESRVRPETIAAENVLHDMGVISMFSSDSQAMGRVGENWLRVVQTAHAMKVARGKLPEDSDGNDNFRVLRYVAKLTINPAIAHGVSHIIGSVEVGKMADLVLWDPRSFGAKPKMVIKGGMINWALMGDPNASLPTPQPVFYRPMFGAMGKTLQDTCATFVSQAALDDGVKEKAGLERQVIAINNCRSVTKRDLVRNSATPHIEVDPETFAVKVDGEHATCNPVTIAVMNQKYFFG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Cytoplasmic

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
132 145 ProSitePatterns PS01120 Urease nickel ligands signature.
132 145 InterPro IPR029754 Urease nickel binding site
130 459 Pfam PF01979 Amidohydrolase family
130 459 InterPro IPR006680 Amidohydrolase-related
2 572 Hamap MF_01953 Urease subunit alpha [ureC].
2 572 InterPro IPR005848 Urease, alpha subunit
414 484 SUPERFAMILY SSF51338 Composite domain of metallo-dependent hydrolases
414 484 InterPro IPR011059 Metal-dependent hydrolase, composite domain superfamily
134 572 ProSiteProfiles PS51368 Urease domain profile.
134 572 InterPro IPR017951 Urease alpha subunit, C-terminal
4 571 NCBIfam TIGR01792 urease subunit alpha
4 571 InterPro IPR005848 Urease, alpha subunit
134 570 Gene3D G3DSA:3.20.20.140 -
322 338 ProSitePatterns PS00145 Urease active site.
322 338 InterPro IPR017950 Urease active site
3 571 PANTHER PTHR43440 UREASE
2 182 SUPERFAMILY SSF51338 Composite domain of metallo-dependent hydrolases
2 182 InterPro IPR011059 Metal-dependent hydrolase, composite domain superfamily
135 571 SUPERFAMILY SSF51556 Metallo-dependent hydrolases
135 571 InterPro IPR032466 Metal-dependent hydrolase
3 124 Pfam PF00449 Urease alpha-subunit, N-terminal domain
3 124 InterPro IPR011612 Urease alpha-subunit, N-terminal domain
432 445 PRINTS PR01752 Urea amidohydrolase (urease) protein signature
432 445 InterPro IPR005848 Urease, alpha subunit
406 421 PRINTS PR01752 Urea amidohydrolase (urease) protein signature
406 421 InterPro IPR005848 Urease, alpha subunit
339 355 PRINTS PR01752 Urea amidohydrolase (urease) protein signature
339 355 InterPro IPR005848 Urease, alpha subunit
300 317 PRINTS PR01752 Urea amidohydrolase (urease) protein signature
300 317 InterPro IPR005848 Urease, alpha subunit
4 485 Gene3D G3DSA:2.30.40.10 Urease, subunit C, domain 1
4 485 InterPro IPR011059 Metal-dependent hydrolase, composite domain superfamily
3 570 CDD cd00375 Urease_alpha
3 570 InterPro IPR005848 Urease, alpha subunit

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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.146
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Surrounding area
Pocket 2 P2Rank #2
0.101
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Surrounding area
Pocket 3 P2Rank #3
0.027
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Surrounding area
Pocket 4 P2Rank #4
0.018
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Surrounding area
Pocket 5 P2Rank #5
0.014
Likely same site as FPocket 16 0.8 Å 8 shared residues 100% of smaller site
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #20
0.831
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Surrounding area
Pocket 2 FPocket #16
0.473
Likely same site as P2Rank 5 0.8 Å 8 shared residues 100% of smaller site
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Surrounding area
Pocket 3 FPocket #30
0.25
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Surrounding area
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_A0A2L1BU89
AlphaFold DB full sequence Viewing
ColabFold VK055_4194
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 P07374 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.

Cross-references

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