KpATCC43816 Protein target profile

cytidine and deoxycytidylate deaminase zinc-binding region family protein

Accession: VK055_4780

Gene: AIK83308.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GWF3
Length 152
Pocket druggability (P2Rank · AlphaFold DB model) 0.657
Direct ligand evidence 0 62 total records
Functional annotation 0 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
Hit
Human identity (%)
26.168 Lower values reduce human off-target concern.
Human E-value
5.78e-10
Gut microbiome similarity
0.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
97.43 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) 0.657
Structure A0A0H3GWF3
Pocket Pocket 1
Druggability (FPocket) 0.731
Structure A0A0H3GWF3
Pocket Pocket 1
ColabFold model
P2Rank 0.531 · Pocket 1
FPocket 0.302 · Pocket 2
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 16 / 4744 genomes with a hit
Prevalence 0.3%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSAHDRYLQRALVLAKQNIADGGRPFGAVLVRNDEIVAESVNTFHLSGDPTAHAELNAVRDLAARLGSAVLRECVIYASGQPCPMCLSALYLTGVREVFFANSNQDGEPFQLSTAAIYQQLQQPLAQQTLPIHHRPQPEGTELYQRWAERQS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

5
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0047974 Catalysis of the reaction: guanosine + H2O + H+ = xanthosine + NH4+.
  • GO:0006152 The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
53 90 ProSitePatterns PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.
53 90 InterPro IPR016192 APOBEC/CMP deaminase, zinc-binding
1 101 Pfam PF00383 Cytidine and deoxycytidylate deaminase zinc-binding region
1 101 InterPro IPR002125 Cytidine and deoxycytidylate deaminase domain
4 113 PANTHER PTHR11079 CYTOSINE DEAMINASE FAMILY MEMBER
2 125 ProSiteProfiles PS51747 Cytidine and deoxycytidylate deaminases domain profile.
2 125 InterPro IPR002125 Cytidine and deoxycytidylate deaminase domain
2 139 SUPERFAMILY SSF53927 Cytidine deaminase-like
2 139 InterPro IPR016193 Cytidine deaminase-like
1 152 Gene3D G3DSA:3.40.140.10 Cytidine Deaminase, domain 2
8 108 CDD cd01285 nucleoside_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
0.657
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.022
Likely same site as FPocket 1 0.9 Å 9 shared residues 100% of smaller site
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
0.731
Likely same site as P2Rank 2 0.9 Å 9 shared residues 100% of smaller site
Show in viewer
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_A0A0H3GWF3
AlphaFold DB full sequence Viewing
ColabFold VK055_4780
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.

62 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 12 records from similar proteins
Structural ligands 12 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5AZ PDB via homolog 112.1 Da · LogP -1.25 · TPSA 84.7 Open detail RCSB PDB
6AM PDB via homolog Detail RCSB PDB
6AP PDB via homolog Detail RCSB PDB
9MG PDB via homolog Detail RCSB PDB
AZG 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
5AZ RCSB PDB A0QY90 112.1 Da LogP -1.25 TPSA 84.7 ✓ Ro5 ✓ Clean C1=NC(=O)NC(=N1)N
6AM RCSB PDB A0QY90 127.1 Da LogP -1.26 TPSA 110.9 ✓ Ro5 ✓ Clean c1(nc(nc(n1)O)N)N
6AP RCSB PDB Q82Y41 150.1 Da LogP -0.48 TPSA 106.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(nc(n2)N)N
9MG RCSB PDB Q82Y41 165.2 Da LogP -0.35 TPSA 89.8 ✓ Ro5 ✓ Clean Cn1cnc2c1nc(nc2O)N
AZG RCSB PDB Q82Y41 152.1 Da LogP -0.96 TPSA 113.6 ✓ Ro5 ✓ Clean c12c(nc(nc1O)N)nn[nH]2
BZE RCSB PDB A0QY90 187.2 Da LogP 0.70 TPSA 90.7 ✓ Ro5 ✓ Clean c1ccc(cc1)c2nc(nc(n2)N)N
CAC RCSB PDB A0QY90 137.0 Da LogP -0.52 TPSA 40.1 ✓ Ro5 ✓ Clean C[As](=O)(C)[O-]
CTN RCSB PDB Q82Y41 243.2 Da LogP -2.56 TPSA 130.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
CYT RCSB PDB Q82Y41 111.1 Da LogP -0.65 TPSA 71.8 ✓ Ro5 ✓ Clean C1=C(NC(=O)N=C1)N
DUC RCSB PDB Q12178 114.1 Da LogP -0.78 TPSA 58.2 ✓ Ro5 ✓ Clean C1CNC(=O)NC1=O
GNG RCSB PDB Q82Y41 267.2 Da LogP -1.66 TPSA 139.3 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3C[C@@H]([C@H](O3)CO)O)NC(=NC2=O)N
HPY RCSB PDB Q12178 114.1 Da LogP -0.87 TPSA 61.4 ✓ Ro5 ✓ Clean C1=CNC(=O)N[C@H]1O

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.