KpATCC43816 Protein target profile

DNA base-flipping protein

Accession: VK055_2135

Gene: AIK80740.1 ybaZ 3D evidence: ColabFold model Metabolism Not in network
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Length 89
Pocket druggability (P2Rank · ColabFold model) 0.003
Direct ligand evidence 0 51 total records
Functional annotation 0 EC 2 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Structure available ColabFold model Ligand evidence via structure/bioactivity 1 structural and 0 bioactivity records.

Risks to review

Human similarity Top human hit identity: 44.681%. This target also has a predicted binding pocket (FPocket 0.68) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 113 of 4744 screened genomes (2.4%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.68) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant. Best pocket may be a modeling artifact FPocket selected-pocket score 0.68, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

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
Hit
Human identity (%)
44.681 Lower values reduce human off-target concern.
Human E-value
7.97e-06
Gut microbiome similarity
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
46.429 Higher values support similarity to known essential genes.
DEG E-value
2.88e-18 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.44 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

ColabFold / curated 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) 0.003
Structure CB_VK055_2135
Pocket Pocket 1
Druggability (FPocket) 0.683
Structure CB_VK055_2135
Pocket Pocket 4
ColabFold model
P2Rank 0.003 · Pocket 1
FPocket 0.683 · Pocket 4
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 113 / 4744 genomes with a hit
Prevalence 2.4%

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.

MASIPEGYVTTYGEVARLAGSPRAARQVGGVLKRLPEGSTLPWHRVVNRHGDISLTGPDLQRQRQALLAEGVQVSGSGHIDLQHYRWVY

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization
Unknown

Gene Ontology (GO)

2
  • 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:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
1 71 CDD cd06445 ATase
1 71 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
1 89 FunFam G3DSA:1.10.10.10:FF:000148 6-O-methylguanine DNA methyltransferase
2 72 Pfam PF01035 6-O-methylguanine DNA methyltransferase, DNA binding domain
2 72 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
1 89 Gene3D G3DSA:1.10.10.10 -
1 89 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
2 88 PANTHER PTHR42942 6-O-METHYLGUANINE DNA METHYLTRANSFERASE
2 73 SUPERFAMILY SSF46767 Methylated DNA-protein cysteine methyltransferase, C-terminal domain
2 73 InterPro IPR036217 Methylated DNA-protein cysteine methyltransferase, DNA binding domain

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.003
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #4
0.683 Unusual size
Show in viewer
Surrounding area
All structural evidence 0 experimental · 1 predicted

Structural evidence

0 + 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
ColabFold VK055_2135
ColabFold — — full sequence — Viewing

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.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
PBO PDB via homolog 149.2 Da · LogP 2.06 · TPSA 30.0 Open detail RCSB PDB
ZINC100071118 ZINC proposed compound · Tanimoto 0.758 Detail ZINC
ZINC100071122 ZINC proposed compound · Tanimoto 0.758 Detail ZINC
ZINC100083979 ZINC proposed compound · Tanimoto 0.667 Detail ZINC
ZINC2379080 ZINC proposed compound · Tanimoto 0.667 Detail ZINC

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
PBO RCSB PDB
3GYH
Q9UTN9 149.2 Da LogP 2.06 TPSA 30.0 ✓ Ro5 ✓ Clean CCCC(=O)c1cccnc1

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.