Protein profile

KP13_03284

Endonuclease 8 bifunctional protein

Genome: KpKP13

Gene: nei AHE45663.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GU47

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Amino acids 263

Annotations 13

Features 31

PDB binders 7

Druggability 0.243

Overview

Basic information about this protein and its source genome.

Accession: KP13_03284
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: nei AHE45663.1
Status: annotated
Amino acids: 263
Structure source: AlphaFold + ColabFold

3.2.2.- 4.2.99.18

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: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. GO:0000703 Catalysis of the removal oxidized pyrimidine bases by cleaving the N-C1' glycosidic bond between the oxidized pyrimidine and the deoxyribose sugar. The reaction involves formation of a covalent enzyme-pyrimidine base 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 apyrimidinic (AP) site.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 32.773
Human E-value: 3.75e-07
Gut microbiome off-target: hit
Essential (DEG): N
DEG identity (%): 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 95.53

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 0.243

Structure A0A0H3GU47

Pocket Pocket 5

P2Rank 0.074

Structure A0A0H3GU47

Pocket Pocket 1

ColabFold model

FPocket 0.303 · Pocket 7

P2Rank 0.077 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 81 / 4744 genomes with a hit

Normalized 0.017

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 11 GO

Enzyme Commission (EC)

Gene Ontology (GO)

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: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.
GO:0000703 Catalysis of the removal oxidized pyrimidine bases by cleaving the N-C1' glycosidic bond between the oxidized pyrimidine and the deoxyribose sugar. The reaction involves formation of a covalent enzyme-pyrimidine base 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 apyrimidinic (AP) site.
GO:0016799 Catalysis of the hydrolysis of any N-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: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).

Sequence Features

Domain/signature hits from InterPro and related databases.

31 records

Show feature table

Start	End	DB	Term	Name
2	116	CDD	cd08965	EcNei-like_N
2	116	InterPro	IPR044091	Nei, N-terminal
2	110	SMART	SM00898	Fapy_DNA_glyco_2
2	110	InterPro	IPR012319	Formamidopyrimidine-DNA glycosylase, catalytic domain
126	214	SUPERFAMILY	SSF46946	S13-like H2TH domain
126	214	InterPro	IPR010979	Ribosomal protein S13-like, H2TH
226	262	SUPERFAMILY	SSF57716	Glucocorticoid receptor-like (DNA-binding domain)
128	263	Gene3D	G3DSA:1.10.8.50	-
2	104	ProSiteProfiles	PS51068	Formamidopyrimidine-DNA glycosylase catalytic domain profile.
2	104	InterPro	IPR012319	Formamidopyrimidine-DNA glycosylase, catalytic domain
127	263	FunFam	G3DSA:1.10.8.50:FF:000005	Endonuclease 8
238	262	ProSitePatterns	PS01242	Zinc finger FPG-type signature.
238	262	InterPro	IPR015887	DNA glycosylase/AP lyase, zinc finger domain, DNA-binding site
126	221	SMART	SM01232	H2TH_2
126	221	InterPro	IPR015886	DNA glycosylase/AP lyase, H2TH DNA-binding
1	262	PANTHER	PTHR42697	ENDONUCLEASE 8
235	263	Pfam	PF06827	Zinc finger found in FPG and IleRS
235	263	InterPro	IPR010663	Zinc finger, FPG/IleRS-type
2	127	Gene3D	G3DSA:3.20.190.10	-
2	127	InterPro	IPR035937	MutM-like, N-terminal
2	127	FunFam	G3DSA:3.20.190.10:FF:000002	Endonuclease 8
2	125	SUPERFAMILY	SSF81624	N-terminal domain of MutM-like DNA repair proteins
2	125	InterPro	IPR035937	MutM-like, N-terminal
1	263	Hamap	MF_01253	Endonuclease 8 [nei].
1	263	InterPro	IPR023713	Endonuclease VIII
127	205	Pfam	PF06831	Formamidopyrimidine-DNA glycosylase H2TH domain
127	205	InterPro	IPR015886	DNA glycosylase/AP lyase, H2TH DNA-binding
1	103	Pfam	PF01149	Formamidopyrimidine-DNA glycosylase N-terminal domain
1	103	InterPro	IPR012319	Formamidopyrimidine-DNA glycosylase, catalytic domain
229	263	ProSiteProfiles	PS51066	Zinc finger FPG-type profile.
229	263	InterPro	IPR000214	Zinc finger, DNA glycosylase/AP lyase-type

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_A0A0H3GU47	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_03284	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
5				0.243

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				2.31	0.059
2				0.98	0.005

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
7				0.303

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				2.59	0.074

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

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
2ON	6RO2	P42371	168.2 Da LogP -0.07 TPSA 74.4	✓ Ro5	✓ Clean	`c1[nH]c2c(n1)C(=O)NC(=N2)S`
5JL	6ROK	P42371	200.2 Da LogP 0.97 TPSA 80.2	✓ Ro5	✓ Clean	`C12=C(NC(=S)N1)NC(=S)NC2=O`
KB5	6RNM	P42371	167.2 Da LogP 0.22 TPSA 80.5	✓ Ro5	✓ Clean	`c1nc(c2c(n1)[nH]c(n2)S)N`
KBN	6RNR	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	6RNO	P42371	167.2 Da LogP 0.91 TPSA 64.4	✓ Ro5	✓ Clean	`c1c[nH]c2c1C(=O)NC(=S)N2`
KD8	6RP7	P42371	208.2 Da LogP 0.99 TPSA 74.4	✓ Ro5	✓ Clean	`Cc1c(nc2c(n1)C(=O)NC(=S)N2)C`
PED	2OQ4	P50465	200.1 Da LogP -0.77 TPSA 107.2	✓ Ro5	✓ Clean	`CC[C@@H]([C@@H](COP(=O)(O)O)O)O`

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
ZINC5975509	0.654	202.1 Da LogP -2.19 TPSA 127.5	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)CO`
ZINC5606355	0.647	203.1 Da LogP 0.95 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1nc(C(F)(F)F)nc2[nH]cnc12`
ZINC9974955	0.625	215.0 Da LogP 0.41 TPSA 74.4	✓ Ro5	✓ Clean	`O=c1[nH]c(Br)nc2[nH]cnc12`
ZINC2384698	0.621	244.2 Da LogP -0.14 TPSA 105.5	✓ Ro5	✓ Clean	`CCOC(OCC)[C@H](O)COP(=O)(O)O`
ZINC4521532	0.621	244.2 Da LogP -0.14 TPSA 105.5	✓ Ro5	✓ Clean	`CCOC(OCC)[C@@H](O)COP(=O)(O)O`
ZINC4823831	0.600	261.0 Da LogP 0.54 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1ncnc2[nH]c(I)nc12`
ZINC967449	0.600	214.0 Da LogP 0.70 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1ncnc2[nH]c(Br)nc12`
ZINC96034425	0.595	218.1 Da LogP 1.38 TPSA 63.7	✓ Ro5	✓ Clean	`COc1nc(C(F)(F)F)nc2[nH]cnc12`
ZINC2522549	0.586	214.1 Da LogP -1.59 TPSA 124.3	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC4543673	0.586	214.1 Da LogP -1.59 TPSA 124.3	✓ Ro5	✓ Clean	`O=CC[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC4543675	0.586	214.1 Da LogP -1.59 TPSA 124.3	✓ Ro5	✓ Clean	`O=CC[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC4543677	0.586	214.1 Da LogP -1.59 TPSA 124.3	✓ Ro5	✓ Clean	`O=CC[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC222362348	0.583	360.4 Da LogP 4.33 TPSA 74.4	✓ Ro5	✓ Clean	`Cc1ccc(-c2nc3[nH]c(=S)[nH]c(=O)c3nc2-c2ccc(C)cc…`
ZINC4726700	0.579	231.2 Da LogP 1.80 TPSA 66.5	✓ Ro5	✓ Clean	`CCNc1nc(C(F)(F)F)nc2[nH]cnc12`
ZINC17919967	0.563	207.3 Da LogP 1.28 TPSA 80.5	✓ Ro5	✓ Clean	`Cc1nc2[nH]c(=S)nc(N)c2nc1C`
ZINC1532601	0.552	200.1 Da LogP -1.98 TPSA 124.3	✓ Ro5	✓ Clean	`O=C[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC2516111	0.552	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@@H](O)CO`
ZINC2522704	0.552	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@H](O)[C@H](O)[C@@H](O)[C@@H](O)CO`
ZINC32786787	0.552	200.1 Da LogP -1.98 TPSA 124.3	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC3869812	0.552	262.2 Da LogP -3.47 TPSA 167.9	1 viol.	✓ Clean	`O=P(O)(O)OC[C@@H](O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC8614702	0.545	216.3 Da LogP 2.34 TPSA 63.2	✓ Ro5	✓ Clean	`S=c1[nH]c(=S)c2[nH]c(=S)[nH]c2[nH]1`
ZINC301097517	0.537	271.2 Da LogP 2.36 TPSA 57.7	✓ Ro5	✓ Clean	`FC(F)(F)c1nc(N2CCCCC2)c2nc[nH]c2n1`
ZINC4707273	0.537	279.2 Da LogP 3.12 TPSA 66.5	✓ Ro5	✓ Clean	`FC(F)(F)c1nc(Nc2ccccc2)c2nc[nH]c2n1`
ZINC240333519	0.524	285.3 Da LogP 3.12 TPSA 66.5	✓ Ro5	✓ Clean	`FC(F)(F)c1nc(NC2CCCCC2)c2nc[nH]c2n1`
ZINC252550334	0.524	273.3 Da LogP 2.97 TPSA 66.5	✓ Ro5	✓ Clean	`CCC(CC)Nc1nc(C(F)(F)F)nc2[nH]cnc12`
ZINC4726481	0.524	259.2 Da LogP 2.58 TPSA 66.5	✓ Ro5	✓ Clean	`CCCCNc1nc(C(F)(F)F)nc2[nH]cnc12`
ZINC514864831	0.524	278.2 Da LogP 1.55 TPSA 91.8	✓ Ro5	✓ Clean	`O=C(O)CSc1nc(C(F)(F)F)nc2[nH]cnc12`
ZINC1529626	0.516	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1530556	0.516	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532567	0.516	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532851	0.516	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC22116391	0.516	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC30320708	0.516	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC3606137	0.516	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC3869426	0.516	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC3870277	0.516	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC8551307	0.516	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC8551308	0.516	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1556567	0.514	211.3 Da LogP 0.95 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1ncnc2nc(S)[nH]c(=S)c12`
ZINC1670205	0.514	213.2 Da LogP -0.66 TPSA 114.6	✓ Ro5	✓ Clean	`CS(=O)(=O)c1nc2c(N)ncnc2[nH]1`
ZINC2486839	0.514	215.2 Da LogP -0.82 TPSA 134.8	✓ Ro5	✓ Clean	`Nc1ncnc2[nH]c(S(=O)(=O)O)nc12`
ZINC4773403	0.514	211.2 Da LogP 1.60 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1ncnc2[nH]c(-c3ccccc3)nc12`
ZINC6556466	0.514	222.3 Da LogP 1.00 TPSA 63.6	✓ Ro5	✓ Clean	`Cc1nc2[nH]c(=S)n(C)c(=O)c2nc1C`
ZINC5729093	0.514	332.4 Da LogP 3.71 TPSA 74.4	✓ Ro5	✓ Clean	`O=c1[nH]c(=S)[nH]c2nc(-c3ccccc3)c(-c3ccccc3)nc12`
ZINC301069237	0.512	273.2 Da LogP 1.21 TPSA 66.9	✓ Ro5	✓ Clean	`FC(F)(F)c1nc(N2CCOCC2)c2nc[nH]c2n1`
ZINC4726480	0.512	293.3 Da LogP 2.98 TPSA 66.5	✓ Ro5	✓ Clean	`FC(F)(F)c1nc(NCc2ccccc2)c2nc[nH]c2n1`
ZINC167345032	0.500	217.2 Da LogP 1.04 TPSA 80.5	✓ Ro5	✓ Clean	`Nc1ncnc2[nH]c(CC(F)(F)F)nc12`
ZINC186096	0.500	209.3 Da LogP 1.44 TPSA 80.5	✓ Ro5	✓ Clean	`CC(C)Sc1nc2c(N)ncnc2[nH]1`
ZINC222362492	0.500	368.4 Da LogP 3.99 TPSA 74.4	✓ Ro5	✓ Clean	`O=c1[nH]c(=S)[nH]c2nc(-c3ccc(F)cc3)c(-c3ccc(F)c…`
ZINC238628781	0.500	213.2 Da LogP 0.71 TPSA 87.3	✓ Ro5	✓ Clean	`O=c1[nH]c(-c2ccccn2)nc2[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.