Protein profile

KP13_05032

Methylated-DNA--protein-cysteine methyltransferase

Genome: KpKP13

Gene: AHE44793.1 ogt Structure source: AlphaFold + ColabFold UniProt A0A0H3GSX7
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Amino acids 175
Annotations 7
Features 20
PDB binders 3
Druggability 0.069

Overview

Basic information about this protein and its source genome.

Accession
KP13_05032
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE44793.1 ogt
Status
annotated
Amino acids
175
Structure source
AlphaFold + ColabFold
EC
2.1.1.63
GO
GO:0003908 Catalysis of the reaction: DNA (containing 6-O-methylguanine) + (protein)-L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine. 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0006307 The repair of alkylation damage in DNA, e.g. the removal of a non-physiological alkyl group from a nucleobase. This is usually mediated by DNA alkyltransferases. GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
45.536
Human E-value
2.5000000000000002e-21
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
43.312
DEG E-value
2.8200000000000002e-33
Localization
Cytoplasmic
ColabFold pLDDT
94.53

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 0.069
Structure A0A0H3GSX7
Pocket Pocket 9
P2Rank 0.1
Structure A0A0H3GSX7
Pocket Pocket 1
ColabFold model
FPocket 0.094 · Pocket 9
P2Rank 0.032 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 79 / 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.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0003908 Catalysis of the reaction: DNA (containing 6-O-methylguanine) + (protein)-L-cysteine = DNA (without 6-O-methylguanine) + protein S-methyl-L-cysteine.
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0006307 The repair of alkylation damage in DNA, e.g. the removal of a non-physiological alkyl group from a nucleobase. This is usually mediated by DNA alkyltransferases.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
141 147 ProSitePatterns PS00374 Methylated-DNA--protein-cysteine methyltransferase active site.
141 147 InterPro IPR001497 Methylated-DNA-[protein]-cysteine S-methyltransferase, active site
93 171 CDD cd06445 ATase
93 171 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
12 171 Hamap MF_00772 Methylated-DNA--protein-cysteine methyltransferase [ogt].
12 171 InterPro IPR023546 Methylated-DNA--protein-cysteine methyltransferase
8 172 PANTHER PTHR10815 METHYLATED-DNA--PROTEIN-CYSTEINE METHYLTRANSFERASE
90 173 SUPERFAMILY SSF46767 Methylated DNA-protein cysteine methyltransferase, C-terminal domain
90 173 InterPro IPR036217 Methylated DNA-protein cysteine methyltransferase, DNA binding domain
11 96 SUPERFAMILY SSF53155 Methylated DNA-protein cysteine methyltransferase domain
11 96 InterPro IPR036631 Methylated DNA-protein cysteine methyltransferase domain superfamily
88 171 Gene3D G3DSA:1.10.10.10 -
88 171 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
89 172 FunFam G3DSA:1.10.10.10:FF:000337 Methylated-DNA--protein-cysteine methyltransferase
92 171 Pfam PF01035 6-O-methylguanine DNA methyltransferase, DNA binding domain
92 171 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
91 170 NCBIfam TIGR00589 methylated-DNA--[protein]-cysteine S-methyltransferase
91 170 InterPro IPR014048 Methylated-DNA-[protein]-cysteine S-methyltransferase, DNA binding
8 87 Pfam PF02870 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain
8 87 InterPro IPR008332 Methylguanine DNA methyltransferase, ribonuclease-like 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

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_A0A0H3GSX7
AlphaFold — — full sequence — Viewing
ColabFold KP13_05032
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

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 1.83 0.035

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.

53 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
ETW
6GA0
Q97VW7 479.5 Da LogP 5.21 TPSA 116.8 1 viol. ✓ Clean Cc1ccc(cc1)CNC(=O)c2ccc(c(c2)C(=O)O)C3=C4C=CC(=…
OGQ
6Y8P
E5BBQ0 534.6 Da LogP 5.24 TPSA 85.8 2 viol. ✓ Clean Cc1ccc(cc1)CNC(=O)c2ccc(c(c2)C3=C4C=CC(=[N+](C)…
PBO
3GYH
Q9UTN9 149.2 Da LogP 2.06 TPSA 30.0 ✓ Ro5 ✓ Clean CCCC(=O)c1cccnc1

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.