Protein target profile

VK055_4005

urease subunit gamma

Genome: KpATCC43816 Gene: ureA AIK82552.1 3D evidence: Experimental + ColabFold model Metabolism 2 reactions UniProt Q02943

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Length 100

Pocket druggability 0.492

Metabolic reactions 2

Chokepoint No

Direct ligand evidence 0 52 total records

Functional annotation 1 EC 5 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.

Main supporting evidence

Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Central metabolic position More central than 90.4% of genes in this genome. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Moderate predicted binding pocket FPocket selected-pocket score 0.49. This supports review but is not experimental validation. Review the complete evidence below

Risks to review

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: No hit
Gut microbiome similarity: 7.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 63.0 Higher values support similarity to known essential genes.
DEG E-value: 2.47e-43 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 97.78 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 0.492

Structure 8HCN

Pocket Pocket 2

P2Rank

Structure 8HCN

Pocket No pockets

ColabFold model

FPocket 0.688 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 359 / 4744 genomes with a hit

Prevalence 7.6%

Cross-references

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

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

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MELTPREKDKLLLFTAALVAERRLARGLKLNYPESVALISAFIMEGARDGKSVASLMEEGRHVLTREQVMEGVPEMIPDIQVEATFPDGSKLVTVHNPII

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

3.5.1.5

Gene Ontology (GO)

GO:0043419 The chemical reactions and pathways resulting in the breakdown of urea, the water soluble compound O=C-(NH2)2.
GO:0016151 Binding to a nickel (Ni) cation.
GO:0009039 Catalysis of the reaction: urea + 2 H2O + H+ = hydrogencarbonate + 2 NH4+.
GO:0019627 The chemical reactions and pathways involving urea, the water soluble compound O=C-(NH2)2.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records

Show feature table

Start	End	DB	Term	Name
1	99	NCBIfam	TIGR00193	urease subunit gamma
1	99	InterPro	IPR002026	Urease, gamma/gamma-beta subunit
4	99	CDD	cd00390	Urease_gamma
4	99	InterPro	IPR002026	Urease, gamma/gamma-beta subunit
1	10	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	100	PIRSF	PIRSF001223	Urease_gamma
1	100	InterPro	IPR012010	Urease, gamma subunit
1	100	Hamap	MF_00739	Urease subunit gamma [ureA].
1	27	Phobius	SIGNAL_PEPTIDE	Signal peptide region
11	19	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	99	PANTHER	PTHR33569	UREASE
20	27	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	99	Pfam	PF00547	Urease, gamma subunit
1	100	Gene3D	G3DSA:3.30.280.10	-
1	100	InterPro	IPR036463	Urease, gamma subunit superfamily
1	99	SUPERFAMILY	SSF54111	Urease, gamma-subunit
1	99	InterPro	IPR036463	Urease, gamma subunit superfamily
28	100	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.

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

0.492

Show in viewer

Surrounding area

Site 2 FPocket #1

0.256

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 8HCN	X-ray	—	A	—	PDBe RCSB PDBj File	Viewing
ColabFold VK055_4005	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.

52 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 2 records from similar proteins

Structural ligands 2 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

DBX PDB via homolog 190.2 Da · LogP 0.34 · TPSA 94.8 Open detail RCSB PDB

HQE PDB via homolog Detail RCSB PDB

ZINC13558894 ZINC proposed compound · Tanimoto 0.727 Detail ZINC

ZINC1700194 ZINC proposed compound · Tanimoto 0.654 Detail ZINC

ZINC2570177 ZINC proposed compound · Tanimoto 0.630 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
DBX RCSB PDB	5FSD	P41022	190.2 Da LogP 0.34 TPSA 94.8	✓ Ro5	✓ Clean	`c1cc(c(cc1O)S(=O)(=O)O)O`
HQE RCSB PDB	5FSE	P41022	110.1 Da LogP 1.10 TPSA 40.5	✓ Ro5	✓ Clean	`c1cc(ccc1O)O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC13558894 ZINC	0.727	262.3 Da LogP 4.43 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(-c2ccc(-c3ccc(O)cc3)cc2)cc1`
ZINC1700194 ZINC	0.654	254.2 Da LogP -0.11 TPSA 129.0	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(O)c(S(=O)(=O)O)c1`
ZINC2570177 ZINC	0.630	208.6 Da LogP 1.29 TPSA 74.6	✓ Ro5	✓ Clean	`O=S(=O)(O)c1cc(Cl)ccc1O`
ZINC391103 ZINC	0.615	220.0 Da LogP 2.00 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1ccc(I)cc1`
ZINC1601787 ZINC	0.609	270.2 Da LogP -0.41 TPSA 149.2	✓ Ro5	✓ Clean	`O=S(=O)(O)c1cc(O)c(S(=O)(=O)O)cc1O`
ZINC1621206 ZINC	0.607	230.3 Da LogP 1.94 TPSA 74.6	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc(O)c(S(=O)(=O)O)c1`
ZINC2510090 ZINC	0.586	202.2 Da LogP 0.45 TPSA 91.7	✓ Ro5	✓ Clean	`O=Cc1ccc(O)c(S(=O)(=O)O)c1`
ZINC34049542 ZINC	0.583	270.2 Da LogP -0.41 TPSA 149.2	✓ Ro5	✓ Clean	`O=S(=O)(O)c1cc(S(=O)(=O)O)c(O)cc1O`
ZINC12428972 ZINC	0.571	214.2 Da LogP 3.51 TPSA 65.2	✓ Ro5	Alert	`Oc1ccc(/N=N/c2ccc(O)cc2)cc1`
ZINC13319959 ZINC	0.571	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(/C=C\c2ccc(O)cc2)cc1`
ZINC136152 ZINC	0.571	200.2 Da LogP 2.69 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(Cc2ccc(O)cc2)cc1`
ZINC136154 ZINC	0.571	218.3 Da LogP 3.25 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(Sc2ccc(O)cc2)cc1`
ZINC1510311 ZINC	0.571	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(/C=C/c2ccc(O)cc2)cc1`
ZINC1562031 ZINC	0.571	214.3 Da LogP 2.88 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(CCc2ccc(O)cc2)cc1`
ZINC1627219 ZINC	0.571	208.6 Da LogP 1.29 TPSA 74.6	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ccc(O)cc1Cl`
ZINC186362 ZINC	0.571	201.2 Da LogP 2.84 TPSA 52.5	✓ Ro5	✓ Clean	`Oc1ccc(Nc2ccc(O)cc2)cc1`
ZINC1875408805 ZINC	0.571	212.2 Da LogP 3.27 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(C=Cc2ccc(O)cc2)cc1`
ZINC254488515 ZINC	0.571	214.2 Da LogP 3.51 TPSA 65.2	✓ Ro5	Alert	`Oc1ccc(N=Nc2ccc(O)cc2)cc1`
ZINC283706 ZINC	0.571	294.3 Da LogP 4.68 TPSA 58.9	✓ Ro5	✓ Clean	`Oc1ccc(Oc2ccc(Oc3ccc(O)cc3)cc2)cc1`
ZINC2924369 ZINC	0.571	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccc(O)cc1`
ZINC33961815 ZINC	0.571	210.2 Da LogP 2.50 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(C#Cc2ccc(O)cc2)cc1`
ZINC39365182 ZINC	0.571	384.4 Da LogP 4.89 TPSA 80.9	✓ Ro5	✓ Clean	`Oc1ccc(C(c2ccc(O)cc2)(c2ccc(O)cc2)c2ccc(O)cc2)c…`
ZINC394643 ZINC	0.571	202.2 Da LogP 2.89 TPSA 49.7	✓ Ro5	✓ Clean	`Oc1ccc(Oc2ccc(O)cc2)cc1`
ZINC4887214 ZINC	0.571	292.3 Da LogP 3.98 TPSA 60.7	✓ Ro5	✓ Clean	`Oc1ccc(C(c2ccc(O)cc2)c2ccc(O)cc2)cc1`
ZINC4963136 ZINC	0.571	311.4 Da LogP 3.90 TPSA 60.7	✓ Ro5	✓ Clean	`Oc1ccc([S+](c2ccc(O)cc2)c2ccc(O)cc2)cc1`
ZINC15768845 ZINC	0.567	422.4 Da LogP 2.17 TPSA 149.2	✓ Ro5	✓ Clean	`O=S(=O)(c1cccc(S(=O)(=O)c2cc(O)ccc2O)c1)c1cc(O)…`
ZINC15769684 ZINC	0.567	498.5 Da LogP 3.84 TPSA 149.2	✓ Ro5	✓ Clean	`O=S(=O)(c1ccc(-c2ccc(S(=O)(=O)c3cc(O)ccc3O)cc2)…`
ZINC36686 ZINC	0.567	250.3 Da LogP 1.93 TPSA 74.6	✓ Ro5	✓ Clean	`O=S(=O)(c1ccccc1)c1cc(O)ccc1O`
ZINC1724272 ZINC	0.548	219.2 Da LogP 0.55 TPSA 117.7	✓ Ro5	✓ Clean	`O=[N+]([O-])c1ccc(O)c(S(=O)(=O)O)c1`
ZINC1691305 ZINC	0.538	320.3 Da LogP 0.74 TPSA 149.2	✓ Ro5	✓ Clean	`O=S(=O)(O)c1cc2cc(S(=O)(=O)O)c(O)cc2cc1O`
ZINC1306 ZINC	0.533	240.3 Da LogP 4.05 TPSA 40.5	✓ Ro5	✓ Clean	`C/C(=C(/C)c1ccc(O)cc1)c1ccc(O)cc1`
ZINC2034791 ZINC	0.533	240.3 Da LogP 4.05 TPSA 40.5	✓ Ro5	✓ Clean	`C/C(=C(\C)c1ccc(O)cc1)c1ccc(O)cc1`
ZINC28449 ZINC	0.533	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(O)cc1`
ZINC332365 ZINC	0.533	318.3 Da LogP 3.56 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(C(=O)c2ccc(O)cc2)cc1`
ZINC4327575 ZINC	0.533	212.2 Da LogP 3.16 TPSA 40.5	✓ Ro5	✓ Clean	`C=C(c1ccc(O)cc1)c1ccc(O)cc1`
ZINC1760471 ZINC	0.531	265.3 Da LogP 1.51 TPSA 100.6	✓ Ro5	✓ Clean	`Nc1ccc(S(=O)(=O)c2cc(O)ccc2O)cc1`
ZINC257795 ZINC	0.531	284.7 Da LogP 2.58 TPSA 74.6	✓ Ro5	✓ Clean	`O=S(=O)(c1ccc(Cl)cc1)c1cc(O)ccc1O`
ZINC36613 ZINC	0.531	264.3 Da LogP 2.24 TPSA 74.6	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)c2cc(O)ccc2O)cc1`
ZINC366453 ZINC	0.531	329.2 Da LogP 2.69 TPSA 74.6	✓ Ro5	✓ Clean	`O=S(=O)(c1ccc(Br)cc1)c1cc(O)ccc1O`
ZINC2187161 ZINC	0.516	224.2 Da LogP 1.79 TPSA 74.6	✓ Ro5	✓ Clean	`O=S(=O)(O)c1cccc2cc(O)ccc12`
ZINC104366597 ZINC	0.515	278.3 Da LogP 3.05 TPSA 99.3	✓ Ro5	Alert	`O=S(=O)(O)c1cc(/N=N\c2ccccc2)ccc1O`
ZINC1719266 ZINC	0.515	265.3 Da LogP 1.90 TPSA 86.6	✓ Ro5	✓ Clean	`O=S(=O)(Nc1ccccc1)c1cc(O)ccc1O`
ZINC4804116 ZINC	0.515	278.3 Da LogP 3.05 TPSA 99.3	✓ Ro5	Alert	`O=S(=O)(O)c1cc(/N=N/c2ccccc2)ccc1O`
ZINC113289810 ZINC	0.500	357.4 Da LogP 3.99 TPSA 99.4	✓ Ro5	✓ Clean	`Oc1ccc(-c2nc(-c3ccc(O)cc3)nc(-c3ccc(O)cc3)n2)cc1`
ZINC1577151 ZINC	0.500	304.3 Da LogP 1.04 TPSA 129.0	✓ Ro5	✓ Clean	`O=S(=O)(O)c1cc(S(=O)(=O)O)c2cc(O)ccc2c1`
ZINC1700211 ZINC	0.500	224.2 Da LogP 1.79 TPSA 74.6	✓ Ro5	✓ Clean	`O=S(=O)(O)c1cccc2ccc(O)cc12`
ZINC2529860 ZINC	0.500	286.2 Da LogP 3.98 TPSA 40.5	✓ Ro5	✓ Clean	`Oc1ccc(C(F)(F)C(F)(F)c2ccc(O)cc2)cc1`
ZINC257798 ZINC	0.500	278.3 Da LogP 2.55 TPSA 74.6	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)c2cc(O)ccc2O)cc1C`
ZINC2579046 ZINC	0.500	296.1 Da LogP 3.66 TPSA 20.2	✓ Ro5	✓ Clean	`Oc1ccc(-c2ccc(I)cc2)cc1`
ZINC27646236 ZINC	0.500	278.3 Da LogP 4.14 TPSA 60.7	✓ Ro5	✓ Clean	`Oc1ccc(-c2ccc(-c3cc(O)cc(O)c3)cc2)cc1`

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.

VK055_4005

Promising target candidate with multiple supporting evidence streams.

Main supporting evidence

Risks to review

Evidence coverage

Prioritization evidence

Off-target risk

Essentiality

Localization

Structure confidence

Binding-site evidence

Cross-references

Sequence

Structure

Pathways

Metabolic context

Sequence

Functional annotations

Enzyme Commission (EC)

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · FPocket

Binding pockets · FPocket

Structural evidence

Ligand evidence