KpATCC43816 Protein target profile

alkB repair system for alkylated DNA and RNA

Accession: VK055_4888

Gene: AIK83415.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GW67
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Length 217
Pocket druggability (P2Rank · AlphaFold DB model) 0.919
Direct ligand evidence 0 95 total records
Functional annotation 1 EC 6 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

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.92. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 4 structural and 41 bioactivity records.

Risks to review

Human similarity Top human hit identity: 32.52%. This target also has a predicted binding pocket (P2Rank 0.92) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 103 of 4744 screened genomes (2.2%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.92) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.86, 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 (%)
32.52 Lower values reduce human off-target concern.
Human E-value
8.74e-14
Gut microbiome similarity
2.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
94.92 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) 0.919
Structure A0A0H3GW67
Pocket Pocket 1
Druggability (FPocket) 0.856
Structure A0A0H3GW67
Pocket Pocket 1
ColabFold model
P2Rank 0.915 · Pocket 1
FPocket 0.618 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 103 / 4744 genomes with a hit
Prevalence 2.2%

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.

MLDLFSDTPPWQEPLAPGAVVLRRFARERAPALLQAIADVASQSPFRQMVTPGGYTMSVAMTNCGALGWTTDRQGYLYAPVDPVTDQTWPPMPAVFHELALAAAAAGGYPEFSPDACLINRYCPGAKLSLHQDKDEQDLRAPIVSVSLGLPAIFQFGGLQRSDPLQRLLLEHGDVVVWGGESRLFYHGIQPLKAGHHPETGDCRYNLTFRQAGGRQY

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Unknown

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0035516 Catalysis of the reaction: a methylated nucleobase within DNA + 2-oxoglutarate + O2 = a nucleobase within DNA + formaldehyde + succinate + CO2. Catalyzes oxidative demethylation of the DNA base lesions N1- methyladenine, N3-methylcytosine, N1-methylguanine, and N3- methylthymine. Can also act of RNA.
  • GO:0008198 Binding to a ferrous iron ion, Fe(II).
  • GO:0035515 Catalysis of the removal of a methyl group from one or more nucleosides within a RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
  • 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.
  • GO:0035513 The removal of the methyl group from one or more nucleotides within an RNA molecule involving oxidation (i.e. electron loss) of one or more atoms.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
113 213 ProSiteProfiles PS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.
113 213 InterPro IPR005123 Oxoglutarate/iron-dependent dioxygenase
11 214 Gene3D G3DSA:2.60.120.590 -
11 214 InterPro IPR037151 Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily
11 216 FunFam G3DSA:2.60.120.590:FF:000005 Alpha-ketoglutarate-dependent dioxygenase AlkB
66 211 PANTHER PTHR16557 ALKYLATED DNA REPAIR PROTEIN ALKB-RELATED
66 211 InterPro IPR004574 Alkylated DNA repair protein AlkB
19 210 Pfam PF13532 2OG-Fe(II) oxygenase superfamily
19 210 InterPro IPR027450 Alpha-ketoglutarate-dependent dioxygenase AlkB-like
15 211 SUPERFAMILY SSF51197 Clavaminate synthase-like

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
0.919
Likely same site as FPocket 1 2.3 Å 26 shared residues 96% of smaller site
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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
0.856 Unusual size
Likely same site as P2Rank 1 2.3 Å 26 shared residues 96% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:101-103
UniProt: Binding site:112-112
UniProt: Binding site:114-114
UniProt: Binding site:116-116
UniProt: Binding site:142-142
UniProt: Binding site:168-168
UniProt: Binding site:185-191
UniProt: Binding site:50-50
UniProt: Binding site:57-59
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_A0A0H3GW67
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_4888
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.

95 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 45 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 41 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AKG PDB via homolog 146.1 Da · LogP -0.50 · TPSA 91.7 Open detail RCSB PDB
OGA PDB via homolog Detail RCSB PDB
SIN PDB via homolog Detail RCSB PDB
XL3 PDB via homolog Detail RCSB PDB
CHEMBL5594860 ChEMBL via homolog · pchembl 7.51 (~30.9 nM) Detail ChEMBL

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
AKG RCSB PDB
5XEG
Q10BI6 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
OGA RCSB PDB
6IMC
P0CB42 147.1 Da LogP -1.73 TPSA 103.7 ✓ Ro5 ✓ Clean C(C(=O)O)NC(=O)C(=O)O
SIN RCSB PDB
6KSF
P0CB42 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
XL3 RCSB PDB
6KSF
P0CB42 76.2 Da LogP 1.33 TPSA 0.0 ✓ Ro5 ✓ Clean CCCS

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.

Sequence

UniProt A0A0H3GW67

Chemistry

ChEMBL CHEMBL5594860 ChEMBL CHEMBL5592755 ChEMBL CHEMBL5589846 ChEMBL CHEMBL5595130 ChEMBL CHEMBL5595043 ChEMBL CHEMBL5591751 ChEMBL CHEMBL5592290 ChEMBL CHEMBL5594481 ChEMBL CHEMBL5593555 ChEMBL CHEMBL5593984 ChEMBL CHEMBL5593030 ChEMBL CHEMBL5591739 ChEMBL CHEMBL5595752 ChEMBL CHEMBL5595276 ChEMBL CHEMBL5593769 ChEMBL CHEMBL5594280 ChEMBL CHEMBL5592202 ChEMBL CHEMBL5595088 ChEMBL CHEMBL5595585 ChEMBL CHEMBL5590866 ChEMBL CHEMBL5592901 ChEMBL CHEMBL5595720 ChEMBL CHEMBL5592192 ChEMBL CHEMBL5592499 ChEMBL CHEMBL5593650 ChEMBL CHEMBL5591761 ChEMBL CHEMBL5592216 ChEMBL CHEMBL5593405 ChEMBL CHEMBL5595815 ChEMBL CHEMBL5593013 ChEMBL CHEMBL5594637 ChEMBL CHEMBL5590799 ChEMBL CHEMBL5595760 ChEMBL CHEMBL5592198 ChEMBL CHEMBL5593535 ChEMBL CHEMBL5595355 ChEMBL CHEMBL5594625 ChEMBL CHEMBL5593235 ChEMBL CHEMBL5595924 ChEMBL CHEMBL5583749 ChEMBL CHEMBL5594690