KpKP13 Protein target profile

Formamidopyrimidine-DNA glycosylase bifunctional protein

Accession: KP13_00188

Gene: AHE42102.1 mutM 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H049
Length 269
Pocket druggability (P2Rank · AlphaFold DB model) 0.435
Direct ligand evidence 0 57 total records
Functional annotation 2 EC 12 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.

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 (%)
28.947 Lower values reduce human off-target concern.
Human E-value
2.44e-06
Gut microbiome similarity
3.7% 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
94.86 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) 0.435
Structure A0A0H3H049
Pocket Pocket 1
Druggability (FPocket) 0.296
Structure A0A0H3H049
Pocket Pocket 6
ColabFold model
P2Rank 0.343 · Pocket 1
FPocket 0.263 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 175 / 4744 genomes with a hit
Prevalence 3.7%

Sequence

Primary amino-acid sequence viewer.

MPELPEVETSRRGIEPHLVGATILHAVVRNGRLRWPVSEEIYRLSDVPVLSVRRRAKYLLLELPDGWIIVHFGMSGSLRILSEELPAEKHDHVDLVMSNGKVLRYTDPRRFGAWLWTRTLEGHPVLAHLGPEPLSDAFNADYLQQKCAKKKTAIKPWLMDNKLVVGVGNIYASESLFSAGIHPDRLASSLSREECEQLVKVIKLVLLRSIEQGGTTLKDFLQSDGKPGYFAQELQVYGRKGEPCRICGTPVVGTKHAQRATFYCRQCQK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 12 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

2

Gene Ontology (GO)

12
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0003684 Binding to damaged DNA.
  • GO:0003906 Catalysis of the cleavage of the C-O-P bond in the AP site created when DNA glycosylase removes a damaged base, involved in the DNA base excision repair pathway (BER).
  • GO:0003676 Binding to a nucleic acid.
  • GO:0006284 In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
  • GO:0019104 Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.
  • 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0008534 Catalysis of the removal of oxidized purine bases by cleaving the N-C1' glycosidic bond between the oxidized purine and the deoxyribose sugar. The reaction involves the formation of a covalent enzyme-substrate intermediate. Release of the enzyme and free base by a beta-elimination or a beta, gamma-elimination mechanism results in the cleavage of the DNA backbone 3' of the apurinic (AP) site.
  • GO:0016799 Catalysis of the hydrolysis of any N-glycosyl bond.
  • GO:0034039 Catalysis of the removal of 8-oxo-7,8-dihydroguanine bases by cleaving the N-C1' glycosidic bond between the oxidized purine and the deoxyribose sugar.
  • GO:0140078 Catalysis of the cleavage of an AP site 3' of the baseless site by a beta-lyase mechanism, leaving an unsaturated aldehyde, termed a 3'-(4-hydroxy-5-phospho-2-pentenal) residue, and a 5'-phosphate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
217 269 SUPERFAMILY SSF57716 Glucocorticoid receptor-like (DNA-binding domain)
129 219 Pfam PF06831 Formamidopyrimidine-DNA glycosylase H2TH domain
129 219 InterPro IPR015886 DNA glycosylase/AP lyase, H2TH DNA-binding
1 114 Pfam PF01149 Formamidopyrimidine-DNA glycosylase N-terminal domain
1 114 InterPro IPR012319 Formamidopyrimidine-DNA glycosylase, catalytic domain
1 269 Hamap MF_00103 Formamidopyrimidine-DNA glycosylase [mutM].
1 269 InterPro IPR020629 Formamidopyrimidine-DNA glycosylase
131 269 Gene3D G3DSA:1.10.8.50 -
1 269 PANTHER PTHR22993 FORMAMIDOPYRIMIDINE-DNA GLYCOSYLASE
2 128 Gene3D G3DSA:3.20.190.10 -
2 128 InterPro IPR035937 MutM-like, N-terminal
235 269 ProSiteProfiles PS51066 Zinc finger FPG-type profile.
235 269 InterPro IPR000214 Zinc finger, DNA glycosylase/AP lyase-type
2 128 FunFam G3DSA:3.20.190.10:FF:000001 Formamidopyrimidine-DNA glycosylase
131 269 FunFam G3DSA:1.10.8.50:FF:000003 Formamidopyrimidine-DNA glycosylase
2 138 SUPERFAMILY SSF81624 N-terminal domain of MutM-like DNA repair proteins
2 138 InterPro IPR035937 MutM-like, N-terminal
244 268 ProSitePatterns PS01242 Zinc finger FPG-type signature.
244 268 InterPro IPR015887 DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site
241 269 Pfam PF06827 Zinc finger found in FPG and IleRS
241 269 InterPro IPR010663 Zinc finger, FPG/IleRS-type
130 222 SUPERFAMILY SSF46946 S13-like H2TH domain
130 222 InterPro IPR010979 Ribosomal protein S13-like, H2TH
2 116 CDD cd08966 EcFpg-like_N
2 112 ProSiteProfiles PS51068 Formamidopyrimidine-DNA glycosylase catalytic domain profile.
2 112 InterPro IPR012319 Formamidopyrimidine-DNA glycosylase, catalytic domain
129 221 SMART SM01232 H2TH_2
129 221 InterPro IPR015886 DNA glycosylase/AP lyase, H2TH DNA-binding
1 268 NCBIfam TIGR00577 DNA-formamidopyrimidine glycosylase
1 268 InterPro IPR020629 Formamidopyrimidine-DNA glycosylase
2 115 SMART SM00898 Fapy_DNA_glyco_2
2 115 InterPro IPR012319 Formamidopyrimidine-DNA glycosylase, catalytic 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.

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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
0.435
Likely same site as FPocket 6 7.2 Å 5 shared residues 71% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.043
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Surrounding area
Pocket 3 P2Rank #3
0.004
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #6
0.296
Likely same site as P2Rank 1 7.2 Å 5 shared residues 71% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:2-2 Schiff-base intermediate with DNA
UniProt: Active site:259-259 Proton donor; for delta-elimination activity
UniProt: Active site:3-3 Proton donor
UniProt: Active site:57-57 Proton donor; for beta-elimination activity
UniProt: Binding site:109-109
UniProt: Binding site:150-150
UniProt: Binding site:90-90
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_A0A0H3H049
AlphaFold DB full sequence Viewing
ColabFold KP13_00188
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2ON PDB via homolog 168.2 Da · LogP -0.07 · TPSA 74.4 Open detail RCSB PDB
5JL PDB via homolog Detail RCSB PDB
KB5 PDB via homolog Detail RCSB PDB
KBN PDB via homolog Detail RCSB PDB
KBQ 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
2ON RCSB PDB P42371 168.2 Da LogP -0.07 TPSA 74.4 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)C(=O)NC(=N2)S
5JL RCSB PDB P42371 200.2 Da LogP 0.97 TPSA 80.2 ✓ Ro5 ✓ Clean C12=C(NC(=S)N1)NC(=S)NC2=O
KB5 RCSB PDB P42371 167.2 Da LogP 0.22 TPSA 80.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)[nH]c(n2)S)N
KBN RCSB PDB P42371 220.2 Da LogP 1.66 TPSA 54.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(nc(n2)C(F)(F)F)S
KBQ RCSB PDB P42371 167.2 Da LogP 0.91 TPSA 64.4 ✓ Ro5 ✓ Clean c1c[nH]c2c1C(=O)NC(=S)N2
KD8 RCSB PDB P42371 208.2 Da LogP 0.99 TPSA 74.4 ✓ Ro5 ✓ Clean Cc1c(nc2c(n1)C(=O)NC(=S)N2)C
PED RCSB PDB P50465 200.1 Da LogP -0.77 TPSA 107.2 ✓ Ro5 ✓ Clean CC[C@@H]([C@@H](COP(=O)(O)O)O)O

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.