Protein profile

PA1686

DNA-3-methyladenine glycosidase II

Genome: NC_002516.2

Gene: PA1686 alkA Structure source: AlphaFold UniProt Q9I339

Export view

Amino acids 297

Annotations 10

Features 20

PDB binders 5

Druggability 0.89

Overview

Basic information about this protein and its source genome.

Accession: PA1686
Assembly: Pseudomonas aeruginosa PAO1, complete genome
Gene: PA1686 alkA
Status: annotated
Amino acids: 297
Structure source: AlphaFold

3.2.2.21

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Gut microbiome off-target: hit
Essential (DEG): N
Localization: Unknown

Selected Druggability evidence

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 0.89

Structure –

Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

3.2.2.21

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
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.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
127	243	FunFam	G3DSA:1.10.340.30:FF:000008	DNA-3-methyladenine glycosylase 2
9	126	SMART	SM01009	AlkA_N_2
9	126	InterPro	IPR010316	DNA-3-methyladenine glycosylase AlkA, N-terminal
117	293	SUPERFAMILY	SSF48150	DNA-glycosylase
117	293	InterPro	IPR011257	DNA glycosylase
128	293	CDD	cd00056	ENDO3c
128	293	InterPro	IPR003265	HhH-GPD domain
79	291	PANTHER	PTHR43003	DNA-3-METHYLADENINE GLYCOSYLASE
245	296	Gene3D	G3DSA:1.10.1670.10	-
245	296	InterPro	IPR023170	Helix-hairpin-helix, base-excision DNA repair, C-terminal
9	107	SUPERFAMILY	SSF55945	TATA-box binding protein-like
9	126	Gene3D	G3DSA:3.30.310.20	-
9	126	InterPro	IPR037046	DNA-3-methyladenine glycosylase AlkA, N-terminal domain superfamily
132	259	Pfam	PF00730	HhH-GPD superfamily base excision DNA repair protein
132	259	InterPro	IPR003265	HhH-GPD domain
128	243	Gene3D	G3DSA:1.10.340.30	Hypothetical protein; domain 2
136	294	SMART	SM00478	endo3end
136	294	InterPro	IPR003265	HhH-GPD domain
10	126	Pfam	PF06029	AlkA N-terminal domain
10	126	InterPro	IPR010316	DNA-3-methyladenine glycosylase AlkA, N-terminal

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...

Legend High Medium Low

Structural evidence

0 + 1

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

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold PA1686	AlphaFold	—	—	full sequence	—	Viewing

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				0.89

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.

47 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`
ANG	1LWV	O15527	166.1 Da LogP -1.19 TPSA 126.5	✓ Ro5	✓ Clean	`c12c([nH]c(n1)N)N=C(NC2=O)N`
BRG	1LWW	O15527	230.0 Da LogP -0.01 TPSA 100.5	✓ Ro5	✓ Clean	`c12c(nc([nH]1)Br)N=C(NC2=O)N`
OXG	1HU0	O15527	165.1 Da LogP -2.28 TPSA 113.6	✓ Ro5	✓ Clean	`C12=NC(=O)N=C1N=C(NC2=O)N`
S5Y	6W0M	O15527	150.2 Da LogP 0.97 TPSA 18.5	✓ Ro5	✓ Clean	`CCOCCOCCS`

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).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1511379	0.704	230.0 Da LogP -0.01 TPSA 100.4	✓ Ro5	✓ Clean	`Nc1nc2[nH]c(Br)nc2c(=O)[nH]1`
ZINC4878369	0.704	277.0 Da LogP -0.17 TPSA 100.4	✓ Ro5	✓ Clean	`Nc1nc2[nH]c(I)nc2c(=O)[nH]1`
ZINC38853515	0.688	226.4 Da LogP 0.90 TPSA 27.7	✓ Ro5	✓ Clean	`SCCOCCOCCOCCS`
ZINC5859031	0.688	294.4 Da LogP 1.13 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCC`
ZINC71773554	0.688	314.5 Da LogP 0.93 TPSA 46.2	✓ Ro5	✓ Clean	`SCCOCCOCCOCCOCCOCCS`
ZINC44583772	0.600	356.5 Da LogP 0.66 TPSA 64.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCS`
ZINC71254558	0.600	444.6 Da LogP 0.70 TPSA 83.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC71254563	0.600	488.6 Da LogP 0.71 TPSA 92.3	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC83253927	0.600	400.5 Da LogP 0.68 TPSA 73.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC83253930	0.600	224.3 Da LogP 0.61 TPSA 36.9	✓ Ro5	✓ Clean	`COCCOCCOCCOCCS`
ZINC90556286	0.600	312.4 Da LogP 0.65 TPSA 55.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCS`
ZINC90556287	0.600	268.4 Da LogP 0.63 TPSA 46.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCS`
ZINC4974293	0.579	280.4 Da LogP 1.08 TPSA 55.4	✓ Ro5	✓ Clean	`CCOCCOCCOCOCCOCCOCC`
ZINC4771751	0.576	227.2 Da LogP 0.90 TPSA 100.4	✓ Ro5	✓ Clean	`Nc1nc2[nH]c(-c3ccccc3)nc2c(=O)[nH]1`
ZINC4643216	0.559	234.3 Da LogP 0.22 TPSA 103.7	✓ Ro5	✓ Clean	`Nc1nc2[nH]c(N3CCCCC3)nc2c(=O)[nH]1`
ZINC5117208	0.543	306.1 Da LogP 1.66 TPSA 100.4	✓ Ro5	✓ Clean	`Nc1nc2[nH]c(-c3ccc(Br)cc3)nc2c(=O)[nH]1`
ZINC88725744	0.543	261.7 Da LogP 1.55 TPSA 100.4	✓ Ro5	✓ Clean	`Nc1nc2[nH]c(-c3ccc(Cl)cc3)nc2c(=O)[nH]1`
ZINC18140551	0.528	255.2 Da LogP 1.64 TPSA 125.2	✓ Ro5	Alert	`Nc1nc2[nH]c(/N=N/c3ccccc3)nc2c(=O)[nH]1`
ZINC4067183	0.528	223.3 Da LogP 0.51 TPSA 100.4	✓ Ro5	✓ Clean	`C=CCSc1nc2c(=O)[nH]c(N)nc2[nH]1`
ZINC4555627	0.528	236.2 Da LogP -0.94 TPSA 112.9	✓ Ro5	✓ Clean	`Nc1nc2[nH]c(N3CCOCC3)nc2c(=O)[nH]1`
ZINC114788106	0.524	297.4 Da LogP -0.04 TPSA 72.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCS`
ZINC1565503710	0.524	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1857523855	0.524	209.3 Da LogP -0.08 TPSA 53.7	✓ Ro5	✓ Clean	`NCCOCCOCCOCCS`
ZINC1857792028	0.524	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057	0.524	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792912	0.524	253.4 Da LogP -0.06 TPSA 62.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCS`
ZINC38917157	0.524	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC5650743	0.524	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC575409817	0.524	385.5 Da LogP -0.01 TPSA 90.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC575432206	0.524	225.3 Da LogP -0.14 TPSA 62.9	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCS`
ZINC6403917	0.524	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446	0.524	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447	0.524	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC1672261	0.522	218.4 Da LogP 4.07 TPSA 9.2	✓ Ro5	✓ Clean	`CCCCCCCCCCOCCS`
ZINC575180644	0.519	330.4 Da LogP 2.23 TPSA 63.2	✓ Ro5	✓ Clean	`CCOP(=O)(CCOCCOCCOCCS)OCC`
ZINC198788572	0.515	248.5 Da LogP 1.35 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1nc(Cl)c2[nH]c(Br)nc2n1`
ZINC88725791	0.514	261.7 Da LogP 1.55 TPSA 100.4	✓ Ro5	✓ Clean	`Nc1nc2[nH]c(-c3ccccc3Cl)nc2c(=O)[nH]1`
ZINC16688007	0.500	446.8 Da LogP 4.03 TPSA 36.9	✓ Ro5	✓ Clean	`CCOCCOCCSCCSCCSCCSCCOCCOCC`
ZINC18158079	0.500	289.7 Da LogP 2.30 TPSA 125.2	✓ Ro5	Alert	`Nc1nc2[nH]c(/N=N/c3ccc(Cl)cc3)nc2c(=O)[nH]1`
ZINC18178302	0.500	334.1 Da LogP 2.41 TPSA 125.2	✓ Ro5	Alert	`Nc1nc2[nH]c(/N=N/c3ccc(Br)cc3)nc2c(=O)[nH]1`
ZINC4301144	0.500	205.0 Da LogP -0.30 TPSA 97.8	✓ Ro5	✓ Clean	`Nc1nc(N)c(Br)c(=O)[nH]1`
ZINC4555844	0.500	273.3 Da LogP 1.52 TPSA 100.4	✓ Ro5	✓ Clean	`Nc1nc2[nH]c(SCc3ccccc3)nc2c(=O)[nH]1`

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.