Protein profile

KP13_02744

A/G-specific adenine glycosylase

Genome: KpKP13

Gene: AHE42688.1 mutY Structure source: AlphaFold + ColabFold UniProt A0A0H3GYC1

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Amino acids 352

Annotations 14

Features 35

PDB binders 1

Druggability 0.477

Overview

Basic information about this protein and its source genome.

Accession: KP13_02744
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE42688.1 mutY
Status: annotated
Amino acids: 352
Structure source: AlphaFold + ColabFold

3.2.2.31

GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0016798 Catalysis of the hydrolysis of any glycosyl bond. 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: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.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 44.907
Human E-value: 2.75e-56
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 93.54

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 0.477

Structure A0A0H3GYC1

Pocket Pocket 1

P2Rank 0.588

Structure A0A0H3GYC1

Pocket Pocket 1

ColabFold model

FPocket 0.359 · Pocket 2

P2Rank 0.624 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 157 / 4744 genomes with a hit

Normalized 0.033

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 13 GO

Enzyme Commission (EC)

3.2.2.31

Gene Ontology (GO)

GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
GO:0016798 Catalysis of the hydrolysis of any glycosyl bond.
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: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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
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:0035485 Binding to a double-stranded DNA region containing an A/G mispair.
GO:0046872 Binding to a metal ion.
GO:0032357 Binding to a DNA region containing an oxidized purine residue.
GO:0000701 Catalysis of the removal of purines present in mismatches, especially opposite oxidized purines, 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 (AP) site.
GO:0006298 A system for the correction of errors in which an incorrect base, which cannot form hydrogen bonds with the corresponding base in the parent strand, is incorporated into the daughter strand. The mismatch repair system promotes genomic fidelity by repairing base-base mismatches, insertion-deletion loops and heterologies generated during DNA replication and recombination.

Sequence Features

Domain/signature hits from InterPro and related databases.

35 records

Show feature table

Start	End	DB	Term	Name
11	213	Gene3D	G3DSA:1.10.1670.10	-
11	213	InterPro	IPR023170	Helix-hairpin-helix, base-excision DNA repair, C-terminal
194	210	ProSitePatterns	PS00764	Endonuclease III iron-sulfur binding region signature.
194	210	InterPro	IPR004035	Endonuclease III, iron-sulphur binding site
6	346	PANTHER	PTHR42944	ADENINE DNA GLYCOSYLASE
6	346	InterPro	IPR044298	Adenine/Thymine-DNA glycosylase
23	137	FunFam	G3DSA:1.10.340.30:FF:000002	Adenine DNA glycosylase
33	190	CDD	cd00056	ENDO3c
33	190	InterPro	IPR003265	HhH-GPD domain
131	213	FunFam	G3DSA:1.10.1670.10:FF:000002	Adenine DNA glycosylase
7	227	SUPERFAMILY	SSF48150	DNA-glycosylase
7	227	InterPro	IPR011257	DNA glycosylase
23	134	Gene3D	G3DSA:1.10.340.30	Hypothetical protein; domain 2
227	349	Gene3D	G3DSA:3.90.79.10	Nucleoside Triphosphate Pyrophosphohydrolase
194	210	Pfam	PF10576	Iron-sulfur binding domain of endonuclease III
194	210	InterPro	IPR003651	Endonuclease III-like, iron-sulphur cluster loop motif
41	192	SMART	SM00478	endo3end
41	192	InterPro	IPR003265	HhH-GPD domain
228	349	FunFam	G3DSA:3.90.79.10:FF:000028	Adenine DNA glycosylase
7	279	NCBIfam	TIGR01084	A/G-specific adenine glycosylase
7	279	InterPro	IPR005760	A/G-specific adenine glycosylase MutY
102	129	Pfam	PF00633	Helix-hairpin-helix motif
102	129	InterPro	IPR000445	Helix-hairpin-helix motif
236	345	Pfam	PF14815	NUDIX domain
236	345	InterPro	IPR029119	Adenine DNA glycosylase, C-terminal
104	133	ProSitePatterns	PS01155	Endonuclease III family signature.
104	133	InterPro	IPR004036	Endonuclease III-like, conserved site-2
38	169	Pfam	PF00730	HhH-GPD superfamily base excision DNA repair protein
38	169	InterPro	IPR003265	HhH-GPD domain
222	346	SUPERFAMILY	SSF55811	Nudix
222	346	InterPro	IPR015797	NUDIX hydrolase-like domain superfamily
237	344	CDD	cd03431	DNA_Glycosylase_C
237	344	InterPro	IPR029119	Adenine DNA glycosylase, C-terminal
193	213	SMART	SM00525	ccc3
193	213	InterPro	IPR003651	Endonuclease III-like, iron-sulphur cluster loop motif

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_A0A0H3GYC1	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02744	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				0.477
22				0.278

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	6.64	0.337
2	5.71	0.276
3	2.56	0.072
4	1.18	0.01

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
2				0.359
8				0.269

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	6.98	0.361
2	6.31	0.317
3	2.19	0.052
4	1.79	0.034

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.

5 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
ADE	1MUD	P17802	135.1 Da LogP -0.06 TPSA 80.5	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)c(ncn2)N`

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
ZINC43463386	0.533	261.0 Da LogP 0.54 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1nc(I)nc2[nH]cnc12`
ZINC4552271	0.533	237.5 Da LogP 2.18 TPSA 54.5	✓ Ro5	✓ Clean	`ClC(Cl)(Cl)c1ncnc2[nH]cnc12`
ZINC4707072	0.533	214.0 Da LogP 0.70 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1nc(Br)nc2[nH]cnc12`
ZINC5543260	0.500	200.2 Da LogP -0.40 TPSA 108.8	✓ Ro5	✓ Clean	`O=S(=O)(O)c1ncnc2[nH]cnc12`

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.