Protein profile

KP13_00947

Alpha-ketoglutarate-dependent dioxygenase alkB

Genome: KpKP13

Gene: alkB AHE43525.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GW67
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Amino acids 217
Annotations 7
Features 10
PDB binders 4
Druggability 0.856

Overview

Basic information about this protein and its source genome.

Accession
KP13_00947
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
alkB AHE43525.1
Status
annotated
Amino acids
217
Structure source
AlphaFold + ColabFold
EC
1.14.11.33
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0035516 Catalysis of the reaction: a methylated nucleobase within DNA + 2-oxoglutarate + O2 = a nucleobase within DNA + formaldehyde + succinate + CO2. Catalyzes oxidative demethylation of the DNA base lesions N1- methyladenine, N3-methylcytosine, N1-methylguanine, and N3- methylthymine. Can also act of RNA. GO:0008198 Binding to a ferrous iron ion, Fe(II). GO:0035515 Catalysis of the removal of a methyl group from one or more nucleosides within a RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms. 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:0035513 The removal of the methyl group from one or more nucleotides within an RNA molecule involving oxidation (i.e. electron loss) of one or more atoms.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
32.52
Human E-value
4.06e-14
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Unknown
ColabFold pLDDT
94.8

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 0.856
Structure A0A0H3GW67
Pocket Pocket 1
P2Rank 0.919
Structure A0A0H3GW67
Pocket Pocket 1
ColabFold model
FPocket 0.941 · Pocket 1
P2Rank 0.89 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 103 / 4744 genomes with a hit
Normalized 0.022

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0035516 Catalysis of the reaction: a methylated nucleobase within DNA + 2-oxoglutarate + O2 = a nucleobase within DNA + formaldehyde + succinate + CO2. Catalyzes oxidative demethylation of the DNA base lesions N1- methyladenine, N3-methylcytosine, N1-methylguanine, and N3- methylthymine. Can also act of RNA.
  • GO:0008198 Binding to a ferrous iron ion, Fe(II).
  • GO:0035515 Catalysis of the removal of a methyl group from one or more nucleosides within a RNA molecule involving the oxidation (i.e. electron loss) of one or more atoms.
  • 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:0035513 The removal of the methyl group from one or more nucleotides within an RNA molecule involving oxidation (i.e. electron loss) of one or more atoms.

Sequence Features

Domain/signature hits from InterPro and related databases.

10 records
Show feature table
Start End DB Term Name
19 210 Pfam PF13532 2OG-Fe(II) oxygenase superfamily
19 210 InterPro IPR027450 Alpha-ketoglutarate-dependent dioxygenase AlkB-like
67 211 PANTHER PTHR16557 ALKYLATED DNA REPAIR PROTEIN ALKB-RELATED
67 211 InterPro IPR004574 Alkylated DNA repair protein AlkB
11 216 FunFam G3DSA:2.60.120.590:FF:000005 Alpha-ketoglutarate-dependent dioxygenase AlkB
11 214 Gene3D G3DSA:2.60.120.590 -
11 214 InterPro IPR037151 Alpha-ketoglutarate-dependent dioxygenase AlkB-like superfamily
15 211 SUPERFAMILY SSF51197 Clavaminate synthase-like
113 213 ProSiteProfiles PS51471 Fe(2+) 2-oxoglutarate dioxygenase domain profile.
113 213 InterPro IPR005123 Oxoglutarate/iron-dependent dioxygenase

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

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_A0A0H3GW67
AlphaFold — — full sequence — Viewing
ColabFold KP13_00947
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 0.856

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 23.97 0.894
2 3.26 0.114

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.

95 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
AKG
5XEG
Q10BI6 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
OGA
6IMC
P0CB42 147.1 Da LogP -1.73 TPSA 103.7 ✓ Ro5 ✓ Clean C(C(=O)O)NC(=O)C(=O)O
SIN
6KSF
P0CB42 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
XL3
6KSF
P0CB42 76.2 Da LogP 1.33 TPSA 0.0 ✓ Ro5 ✓ Clean CCCS

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.