KpATCC43816 Protein target profile

deoxycytidine triphosphate deaminase

Accession: VK055_5009

Gene: dcd AIK83535.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GQQ4
Length 193
Pocket druggability (P2Rank · AlphaFold DB model) 0.35
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 56 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.

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
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
27.451 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
98.36 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) 0.35
Structure A0A0H3GQQ4
Pocket Pocket 1
Druggability (FPocket) 0.538
Structure A0A0H3GQQ4
Pocket Pocket 1
ColabFold model
P2Rank 0.369 · Pocket 1
FPocket 0.263 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 142 / 4744 genomes with a hit
Prevalence 3.0%

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 99.0% of genes in this genome, no human homolog detected.

Relative network centrality 99.0% more central than 99.0% of genes in this genome
Chokepoint Not a chokepoint
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.

MRLCDRDIEAWLDEGRLAINPRPPVERINGATVDVRLGNKFRTFRGHTAPFIDLSGPKAEVSAALDRVMSEEIVLPEGEAFFLHPGELALAVTYESVTLPADLVGWLDGRSSLARLGLMVHVTAHRIDPGWSGCIVLEFYNSGKLPLALRPGMPIGALSFEPLSGPAARPYNRREDAKYRDQQGAVASRIDKD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0008829 Catalysis of the reaction: dCTP + H2O + H+ = dUTP + NH4+.
  • GO:0006229 The chemical reactions and pathways resulting in the formation of dUTP, deoxyuridine (5'-)triphosphate.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • GO:0006226 The chemical reactions and pathways resulting in the formation of dUMP, deoxyuridine monophosphate (2'-deoxyuridine 5'-phosphate).
  • GO:0015949 The chemical reactions and pathways by which a nucleobase, nucleoside or nucleotide small molecule is synthesized from another nucleobase, nucleoside or nucleotide small molecule.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
171 193 MobiDBLite mobidb-lite consensus disorder prediction
77 160 CDD cd07557 trimeric_dUTPase
77 160 InterPro IPR033704 dUTPase, trimeric
2 190 NCBIfam TIGR02274 dCTP deaminase
2 190 InterPro IPR011962 dCTP deaminase
1 193 Gene3D G3DSA:2.70.40.10 -
1 193 InterPro IPR036157 dUTPase-like superfamily
169 193 MobiDBLite mobidb-lite consensus disorder prediction
1 190 Hamap MF_00146 dCTP deaminase, dUMP-forming [dcd].
1 190 InterPro IPR011962 dCTP deaminase
79 185 Pfam PF00692 dUTPase
79 185 InterPro IPR029054 dUTPase-like
1 193 SUPERFAMILY SSF51283 dUTPase-like
2 192 PANTHER PTHR42680 DCTP DEAMINASE
1 193 FunFam G3DSA:2.70.40.10:FF:000003 dCTP deaminase

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
0.35
Likely same site as FPocket 1 1.7 Å 14 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.062
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.538 Unusual size
Likely same site as P2Rank 1 1.7 Å 14 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:138-138 Proton donor/acceptor
UniProt: Binding site:110-115
UniProt: Binding site:128-128
UniProt: Binding site:136-138
UniProt: Binding site:171-171
UniProt: Binding site:178-178
UniProt: Binding site:182-182
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_A0A0H3GQQ4
AlphaFold DB full sequence Viewing
ColabFold VK055_5009
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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
DCP PDB via homolog 467.2 Da · LogP -1.18 · TPSA 250.2 Open detail RCSB PDB
DUP PDB via homolog Detail RCSB PDB
DUT PDB via homolog Detail RCSB PDB
POP PDB via homolog Detail RCSB PDB
TTP 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
DCP RCSB PDB P28248 467.2 Da LogP -1.18 TPSA 250.2 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=…
DUP RCSB PDB Q57872 467.2 Da LogP -1.90 TPSA 246.9 1 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@](=O…
DUT RCSB PDB P28248 468.1 Da LogP -1.47 TPSA 244.1 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO[P@@](=…
POP RCSB PDB Q57872 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=O)(O)[O-]
TTP RCSB PDB P28248 482.2 Da LogP -1.16 TPSA 244.1 2 viol. ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…
TYD RCSB PDB P28248 402.2 Da LogP -1.28 TPSA 197.6 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO[P@]…

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.