Protein profile

KP13_03142

DNA-3-methyladenine glycosylase 2

Genome: KpKP13

Gene: alkA AHE43643.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVA4

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Amino acids 282

Annotations 12

Features 22

PDB binders 1

Druggability 0.927

Overview

Basic information about this protein and its source genome.

Accession: KP13_03142
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: alkA AHE43643.1
Status: annotated
Amino acids: 282
Structure source: AlphaFold + ColabFold

3.2.2.21

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: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. GO:0003905 Catalysis of the reaction: DNA with alkylated base + H2O = DNA with abasic site + alkylated base. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar to remove an alkylated base, leaving an apyrimidinic or apurinic site. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0032993 A macromolecular complex containing both protein and DNA molecules.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Unknown
ColabFold pLDDT: 96.64

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.927

Structure A0A0H3GVA4

Pocket Pocket 1

P2Rank 0.817

Structure A0A0H3GVA4

Pocket Pocket 1

ColabFold model

FPocket 0.885 · Pocket 1

P2Rank 0.793 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 65 / 4744 genomes with a hit

Normalized 0.014

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 11 GO

Enzyme Commission (EC)

3.2.2.21

Gene Ontology (GO)

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: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.
GO:0003905 Catalysis of the reaction: DNA with alkylated base + H2O = DNA with abasic site + alkylated base. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar to remove an alkylated base, leaving an apyrimidinic or apurinic site.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0032993 A macromolecular complex containing both protein and DNA molecules.
GO:0032131 Binding to an alkylated residue in DNA.
GO:0008725 Catalysis of the reaction: DNA containing 3-methyladenine + H2O = DNA with abasic site + 3-methyladenine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 3-methyladenine and the deoxyribose sugar to remove the 3-methyladenine, leaving an abasic site.
GO:0043916 Catalysis of the reaction: DNA containing 7-methylguanine + H2O = DNA with abasic site + 7-methylguanine. This reaction is the hydrolysis of DNA by cleavage of the N-C1' glycosidic bond between the damaged DNA 7-methylguanine and the deoxyribose sugar to remove the 7-methylguanine, leaving an abasic site.
GO:0006285 The formation of an AP site, a deoxyribose sugar with a missing base, by DNA glycosylase which recognizes an altered base in DNA and catalyzes its hydrolytic removal. This sugar phosphate is the substrate recognized by the AP endonuclease, which cuts the DNA phosphodiester backbone at the 5' side of the altered site to leave a gap which is subsequently repaired.
GO:0006307 The repair of alkylation damage in DNA, e.g. the removal of a non-physiological alkyl group from a nucleobase. This is usually mediated by DNA alkyltransferases.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records

Show feature table

Start	End	DB	Term	Name
113	230	FunFam	G3DSA:1.10.340.30:FF:000008	DNA-3-methyladenine glycosylase 2
231	281	Gene3D	G3DSA:1.10.1670.10	-
231	281	InterPro	IPR023170	Helix-hairpin-helix, base-excision DNA repair, C-terminal
113	230	Gene3D	G3DSA:1.10.340.30	Hypothetical protein; domain 2
2	112	Gene3D	G3DSA:3.30.310.20	-
2	112	InterPro	IPR037046	DNA-3-methyladenine glycosylase AlkA, N-terminal domain superfamily
2	97	SUPERFAMILY	SSF55945	TATA-box binding protein-like
114	273	CDD	cd00056	ENDO3c
114	273	InterPro	IPR003265	HhH-GPD domain
214	238	ProSitePatterns	PS00516	Alkylbase DNA glycosidases alkA family signature.
214	238	InterPro	IPR000035	Alkylbase DNA glycosidase, conserved site
1	112	SMART	SM01009	AlkA_N_2
1	112	InterPro	IPR010316	DNA-3-methyladenine glycosylase AlkA, N-terminal
130	276	SMART	SM00478	endo3end
130	276	InterPro	IPR003265	HhH-GPD domain
3	112	Pfam	PF06029	AlkA N-terminal domain
3	112	InterPro	IPR010316	DNA-3-methyladenine glycosylase AlkA, N-terminal
118	241	Pfam	PF00730	HhH-GPD superfamily base excision DNA repair protein
118	241	InterPro	IPR003265	HhH-GPD domain
101	275	SUPERFAMILY	SSF48150	DNA-glycosylase
101	275	InterPro	IPR011257	DNA glycosylase
101	274	PANTHER	PTHR43003	DNA-3-METHYLADENINE GLYCOSYLASE

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GVA4	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03142	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.927
18				0.539

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				14.11	0.712
2				4.2	0.171

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.885
12				0.225

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	14.23	0.716
2	4.16	0.168
3	1.39	0.017
4	0.75	0.002

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.

1 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
7HP	1PVS	P04395	136.1 Da LogP 0.06 TPSA 74.7	✓ Ro5	✓ Clean	`c1c2c(c(ncn2)O)[nH]n1`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

No virtual-screening candidates for this protein.

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.