Protein profile

KP13_01376

Endonuclease V

Genome: KpKP13

Gene: nfi AHE46923.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GGQ9
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Amino acids 223
Annotations 8
Features 11
PDB binders 2
Druggability 0.701

Overview

Basic information about this protein and its source genome.

Accession
KP13_01376
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
nfi AHE46923.1
Status
annotated
Amino acids
223
Structure source
AlphaFold + ColabFold
EC
3.1.21.7
GO
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:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0043737 Catalysis of the endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5'-phosphate. GO:0000287 Binding to a magnesium (Mg) ion. GO:0016891 Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
48.649
Human E-value
7.84e-18
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.51

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 0.701
Structure A0A0H3GGQ9
Pocket Pocket 1
P2Rank 0.566
Structure A0A0H3GGQ9
Pocket Pocket 1
ColabFold model
FPocket 0.502 · Pocket 1
P2Rank 0.62 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 123 / 4744 genomes with a hit
Normalized 0.026

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • 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:0004519 Catalysis of the cleavage of ester linkages within nucleic acids by creating internal breaks.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0043737 Catalysis of the endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5'-phosphate.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0016891 Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
  • GO:0003727 Binding to single-stranded RNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
6 26 Coils Coil Coil
22 211 PANTHER PTHR28511 ENDONUCLEASE V
22 211 InterPro IPR007581 Endonuclease V
12 206 Pfam PF04493 Endonuclease V
12 206 InterPro IPR007581 Endonuclease V
1 214 FunFam G3DSA:3.30.2170.10:FF:000001 Endonuclease V
3 211 CDD cd06559 Endonuclease_V
3 211 InterPro IPR007581 Endonuclease V
1 214 Gene3D G3DSA:3.30.2170.10 archaeoglobus fulgidus dsm 4304 superfamily
2 216 Hamap MF_00801 Endonuclease V [nfi].
2 216 InterPro IPR007581 Endonuclease V

3D Structure

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

3D visualization script Full viewer

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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_A0A0H3GGQ9
AlphaFold — — full sequence — Viewing
ColabFold KP13_01376
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 0.701

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 6.45 0.325
2 1.28 0.013

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.

52 records

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
TLA
6OZK
Q8C9A2 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O
YES
3GOC
Q82MH6 208.3 Da LogP -1.67 TPSA 101.2 ✓ Ro5 ✓ Clean C(CO)C(CCO)C(CO)(CO)CO

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.