Protein profile

VK055_2468

8-oxo-dGTPase

Genome: KpATCC43816

Gene: AIK81065.1 mutT Structure source: Experimental + ColabFold UniProt A0A1Y0Q4X2
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Amino acids 130
Annotations 9
Features 23
PDB binders 6
Druggability 0.417

Overview

Basic information about this protein and its source genome.

Accession
VK055_2468
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK81065.1 mutT
Status
annotated
Amino acids
130
Structure source
Experimental + ColabFold
EC
3.6.1.55
GO
GO:0008413 Catalysis of the reaction: 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) + H2O = 8-oxo-7,8-dihydroguanosine diphosphate (8-oxo-GDP) + phosphate. 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for transcription. 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:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. GO:0035539 Catalysis of the reaction: 8-oxo-7,8-dihydrodeoxyguanosine-triphosphate (8-oxo-dGTP) + H2O = 8-oxo-7,8-dihydrodeoxyguanosine phosphate (8-oxo-dGMP) + diphosphate. 8-oxo-dGTP is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for DNA synthesis causing transversion mutations. 8-oxo-dGTPase hydrolyses 8-oxo-dGTP to its monophosphate form to prevent the misincorporation of 8-oxo-dGTP into cellular DNA. GO:0044715 Catalysis of the reaction 8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate. GO:0044716 Catalysis of the reaction 8-oxo-GDP + H2O = 8-oxo-GMP + phosphate.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
45.385
DEG E-value
1.26e-36
Localization
Unknown
ColabFold pLDDT
91.86

Selected Druggability evidence

PDB experimental structure

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 0.417
Structure 7SYC
Pocket Pocket 4
P2Rank 0.118
Structure 7SYC
Pocket Pocket 1
ColabFold model
FPocket 0.666 · Pocket 6
P2Rank 0.171 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 110 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0008413 Catalysis of the reaction: 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) + H2O = 8-oxo-7,8-dihydroguanosine diphosphate (8-oxo-GDP) + phosphate. 8-oxo-7,8-dihydroguanosine triphosphate (8-oxo-GTP) is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for transcription.
  • 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:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0035539 Catalysis of the reaction: 8-oxo-7,8-dihydrodeoxyguanosine-triphosphate (8-oxo-dGTP) + H2O = 8-oxo-7,8-dihydrodeoxyguanosine phosphate (8-oxo-dGMP) + diphosphate. 8-oxo-dGTP is the oxidised form of the free guanine nucleotide and can act as a potent mutagenic substrate for DNA synthesis causing transversion mutations. 8-oxo-dGTPase hydrolyses 8-oxo-dGTP to its monophosphate form to prevent the misincorporation of 8-oxo-dGTP into cellular DNA.
  • GO:0044715 Catalysis of the reaction 8-oxo-dGDP + H2O = 8-oxo-dGMP + phosphate.
  • GO:0044716 Catalysis of the reaction 8-oxo-GDP + H2O = 8-oxo-GMP + phosphate.
  • GO:0046872 Binding to a metal ion.
  • GO:0006260 The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by the origin recognition complex, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
1 128 Gene3D G3DSA:3.90.79.10 Nucleoside Triphosphate Pyrophosphohydrolase
33 47 PRINTS PR00502 NUDIX hydrolase family signature
33 47 InterPro IPR020476 NUDIX hydrolase
47 62 PRINTS PR00502 NUDIX hydrolase family signature
47 62 InterPro IPR020476 NUDIX hydrolase
1 129 FunFam G3DSA:3.90.79.10:FF:000014 8-oxo-dGTP diphosphatase MutT
38 59 ProSitePatterns PS00893 Nudix box signature.
38 59 InterPro IPR020084 NUDIX hydrolase, conserved site
2 128 PANTHER PTHR47707 8-OXO-DGTP DIPHOSPHATASE
2 128 InterPro IPR047127 Mutator MutT-like
6 122 Pfam PF00293 NUDIX domain
6 122 InterPro IPR000086 NUDIX hydrolase domain
4 127 CDD cd03425 MutT_pyrophosphohydrolase
2 126 SUPERFAMILY SSF55811 Nudix
2 126 InterPro IPR015797 NUDIX hydrolase-like domain superfamily
1 126 NCBIfam TIGR00586 8-oxo-dGTP diphosphatase MutT
1 126 InterPro IPR003561 Mutator MutT
77 90 PRINTS PR01401 Mutator MutT protein signature
77 90 InterPro IPR003561 Mutator MutT
2 23 PRINTS PR01401 Mutator MutT protein signature
2 23 InterPro IPR003561 Mutator MutT
1 129 ProSiteProfiles PS51462 Nudix hydrolase domain profile.
1 129 InterPro IPR000086 NUDIX hydrolase domain

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

1 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 7SYC
X-ray 2.00 Å A
100.0% 1-130
PDBe RCSB PDBj File
Viewing
ColabFold VK055_2468
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
4 0.417

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 3.33 0.118

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.

56 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
523
5ZRO
A0R2K6 482.2 Da LogP -1.46 TPSA 252.0 1 viol. ✓ Clean CC1=C(NC(=O)[N+](=C1)[C@H]2C[C@@H]([C@H](O2)CO[…
8OG
1PPX
P08337 363.2 Da LogP -2.25 TPSA 205.8 1 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C3=C(C(=O)NC(=N3)N)NC2=…
9L3
5ZRI
A0R2K6 306.2 Da LogP -0.98 TPSA 139.0 ✓ Ro5 ✓ Clean Cc1c[n+](cnc1N)[C@H]2C[C@@H]([C@H](O2)COP(=O)(O…
APC
1TUM
P08337 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DCP
5ZRK
A0R2K6 467.2 Da LogP -1.18 TPSA 250.2 2 viol. ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=NC2=O)N)CO[P@@](=…
TLA
3A6S
P08337 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O

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.