Protein profile

KP13_03919

Pyrimidine monooxygenase RutA

Genome: KpKP13

Gene: AHE45335.1 rutA Structure source: AlphaFold + ColabFold UniProt A0A0H3GQY2
Export view
Amino acids 363
Annotations 8
Features 13
PDB binders 8
Druggability 0.89

Overview

Basic information about this protein and its source genome.

Accession
KP13_03919
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45335.1 rutA
Status
annotated
Amino acids
363
Structure source
AlphaFold + ColabFold
EC
1.14.99.46
GO
GO:0004497 Catalysis of the incorporation of one atom of molecular oxygen (O2) into the substrate and the reduction of the other atom of O2 to water. GO:0006212 The chemical reactions and pathways resulting in the breakdown of uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA. GO:0016705 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor. GO:0008726 Catalysis of the reaction: an alkanesulfonate + O2 + FMNH2 = an aldehyde + sulfite + H2O + FMN. GO:0052614 Catalysis of the reaction: FMNH2 + NADH + O2 + uracil = (Z)-3-ureidoacrylate + FMN + H+ + H2O + NAD+. Can also use thymine as a substrate. GO:0046306 The chemical reactions and pathways resulting in the breakdown of alkanesulfonates, the anion of alkanesulfonic acids, sulfonic acid derivatives containing an aliphatic hydrocarbon group.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.58

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 0.89
Structure A0A0H3GQY2
Pocket Pocket 1
P2Rank 0.98
Structure A0A0H3GQY2
Pocket Pocket 1
ColabFold model
FPocket 0.925 · Pocket 1
P2Rank 0.981 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 56 / 4744 genomes with a hit
Normalized 0.012

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:0004497 Catalysis of the incorporation of one atom of molecular oxygen (O2) into the substrate and the reduction of the other atom of O2 to water.
  • GO:0006212 The chemical reactions and pathways resulting in the breakdown of uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA.
  • GO:0016705 Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
  • GO:0008726 Catalysis of the reaction: an alkanesulfonate + O2 + FMNH2 = an aldehyde + sulfite + H2O + FMN.
  • GO:0052614 Catalysis of the reaction: FMNH2 + NADH + O2 + uracil = (Z)-3-ureidoacrylate + FMN + H+ + H2O + NAD+. Can also use thymine as a substrate.
  • GO:0046306 The chemical reactions and pathways resulting in the breakdown of alkanesulfonates, the anion of alkanesulfonic acids, sulfonic acid derivatives containing an aliphatic hydrocarbon group.
  • GO:0019740 A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary nitrogen source, usually ammonia, and then activates genes to scavenge the last traces of the primary nitrogen source and to transport and metabolize alternative nitrogen sources. The utilization process begins when the cell or organism detects nitrogen levels, includes the activation of genes whose products detect, transport or metabolize nitrogen-containing substances, and ends when nitrogen is incorporated into the cell or organism's metabolism.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
1 360 Hamap MF_01699 Pyrimidine monooxygenase RutA [rutA].
1 360 InterPro IPR019914 Pyrimidine monooxygenase RutA
1 258 CDD cd01094 Alkanesulfonate_monoxygenase
1 354 Gene3D G3DSA:3.20.20.30 -
1 354 InterPro IPR036661 Luciferase-like domain superfamily
1 354 FunFam G3DSA:3.20.20.30:FF:000003 Pyrimidine monooxygenase RutA
1 320 Pfam PF00296 Luciferase-like monooxygenase
1 320 InterPro IPR011251 Luciferase-like domain
1 355 NCBIfam TIGR03612 pyrimidine utilization protein A
1 355 InterPro IPR019914 Pyrimidine monooxygenase RutA
1 354 PANTHER PTHR42847 ALKANESULFONATE MONOOXYGENASE
1 352 SUPERFAMILY SSF51679 Bacterial luciferase-like
1 352 InterPro IPR036661 Luciferase-like domain superfamily

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...

Legend High Medium Low

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_A0A0H3GQY2
AlphaFold — — full sequence — Viewing
ColabFold KP13_03919
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 0.89

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 46.89 0.975
2 2.32 0.059
3 1.54 0.023
4 0.99 0.005

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.

58 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
03S
7K14
Q3K9A1 96.1 Da LogP -0.50 TPSA 54.4 ✓ Ro5 ✓ Clean CS(=O)(=O)O
9WY
5W4Z
A0A3B6UEK8 456.3 Da LogP -1.61 TPSA 208.1 1 viol. ✓ Clean Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC([C@@H]([…
F42
1RHC
O93734 773.6 Da LogP -2.72 TPSA 374.5 3 viol. ✓ Clean C[C@@H](C(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)C(…
FLC
3B4Y
P9WNE1 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
LFN
6ASL
O34974 256.3 Da LogP 0.74 TPSA 80.6 ✓ Ro5 ✓ Clean Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C
RBF
5W4Z
A0A3B6UEK8 376.4 Da LogP -1.72 TPSA 161.6 ✓ Ro5 ✓ Clean Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@…
SIN
7JYB
Q3K9A1 118.1 Da LogP -0.06 TPSA 74.6 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)O
URA
5WAN
P75898 112.1 Da LogP -0.94 TPSA 65.7 ✓ Ro5 ✓ Clean C1=CNC(=O)NC1=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.