Protein profile

KP13_03917

protein rutC

Genome: KpKP13

Gene: AHE45337.1 rutC Structure source: AlphaFold + ColabFold UniProt A0A0H3GL84
Export view
Amino acids 126
Annotations 5
Features 14
PDB binders 3
Druggability 0.559

Overview

Basic information about this protein and its source genome.

Accession
KP13_03917
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45337.1 rutC
Status
annotated
Amino acids
126
Structure source
AlphaFold + ColabFold
EC
3.5.-.-
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0019239 Catalysis of the removal of an amino group from a substrate, producing a substituted or nonsubstituted ammonia (NH4+/NH2R). 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. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
24.39
Human E-value
5.99e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
84.553
DEG E-value
1.19e-76
Localization
Cytoplasmic
ColabFold pLDDT
95.41

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 0.559
Structure A0A0H3GL84
Pocket Pocket 1
P2Rank 0.507
Structure A0A0H3GL84
Pocket Pocket 1
ColabFold model
FPocket 0.689 · Pocket 1
P2Rank 0.553 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 58 / 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 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0019239 Catalysis of the removal of an amino group from a substrate, producing a substituted or nonsubstituted ammonia (NH4+/NH2R).
  • 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.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
1 124 Hamap MF_00831 3-aminoacrylate deaminase RutC [rutC].
1 124 InterPro IPR019898 3-aminoacrylate deaminase RutC
9 121 Pfam PF01042 Endoribonuclease L-PSP
9 121 InterPro IPR006175 YjgF/YER057c/UK114 family
14 120 CDD cd00448 YjgF_YER057c_UK114_family
98 116 ProSitePatterns PS01094 Uncharacterized protein family UPF0076 signature.
98 116 InterPro IPR019897 RidA, conserved site
9 121 PANTHER PTHR11803 2-IMINOBUTANOATE/2-IMINOPROPANOATE DEAMINASE RIDA
2 123 SUPERFAMILY SSF55298 YjgF-like
2 123 InterPro IPR035959 RutC-like superfamily
1 123 Gene3D G3DSA:3.30.1330.40 -
1 123 InterPro IPR035959 RutC-like superfamily
1 123 NCBIfam TIGR03610 pyrimidine utilization protein C
1 123 InterPro IPR019898 3-aminoacrylate deaminase RutC

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_A0A0H3GL84
AlphaFold — — full sequence — Viewing
ColabFold KP13_03917
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 0.559
5 0.002
6 0.002
2 0.001

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 10.98 0.507
2 0.61 0.001

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.

54 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
BEZ
1ONI
P52758 122.1 Da LogP 1.38 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)O
EMC
1QD9
P37552 229.7 Da LogP 0.97 TPSA 0.0 ✓ Ro5 ✓ Clean CC[Hg+]
FLC
3M1X
C4LXT9 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=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.