Protein profile

VK055_1442

pyrimidine utilization protein D

Genome: KpATCC43816

Gene: AIK80063.1 rutD Structure source: AlphaFold + ColabFold UniProt A0A377TPP8
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Amino acids 266
Annotations 5
Features 19
PDB binders 5
Druggability 0.872

Overview

Basic information about this protein and its source genome.

Accession
VK055_1442
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80063.1 rutD
Status
annotated
Amino acids
266
Structure source
AlphaFold + ColabFold
EC
3.5.1.-
GO
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:0016811 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide. GO:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor). 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
28.431
Human E-value
3.97e-06
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
26.562
Localization
Unknown
ColabFold pLDDT
96.76

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 0.872
Structure A0A377TPP8
Pocket Pocket 1
P2Rank 0.939
Structure A0A377TPP8
Pocket Pocket 1
ColabFold model
FPocket 0.836 · Pocket 1
P2Rank 0.948 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 39 / 4744 genomes with a hit
Normalized 0.008

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: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:0016811 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
  • GO:0016746 Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
  • 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.

19 records
Show feature table
Start End DB Term Name
14 119 Pfam PF00561 alpha/beta hydrolase fold
14 119 InterPro IPR000073 Alpha/beta hydrolase fold-1
1 258 Gene3D G3DSA:3.40.50.1820 alpha/beta hydrolase
1 258 InterPro IPR029058 Alpha/Beta hydrolase fold
1 257 NCBIfam TIGR03611 pyrimidine utilization protein D
1 257 InterPro IPR019913 Pyrimidine utilisation protein RutD
98 111 PRINTS PR00111 Alpha/beta hydrolase fold signature
98 111 InterPro IPR000073 Alpha/beta hydrolase fold-1
84 97 PRINTS PR00111 Alpha/beta hydrolase fold signature
84 97 InterPro IPR000073 Alpha/beta hydrolase fold-1
39 54 PRINTS PR00111 Alpha/beta hydrolase fold signature
39 54 InterPro IPR000073 Alpha/beta hydrolase fold-1
201 215 PRINTS PR00111 Alpha/beta hydrolase fold signature
201 215 InterPro IPR000073 Alpha/beta hydrolase fold-1
9 253 SUPERFAMILY SSF53474 alpha/beta-Hydrolases
9 253 InterPro IPR029058 Alpha/Beta hydrolase fold
13 255 PANTHER PTHR43433 HYDROLASE, ALPHA/BETA FOLD FAMILY PROTEIN
1 258 Hamap MF_00832 Putative carbamate hydrolase RutD [rutD].
1 258 InterPro IPR019913 Pyrimidine utilisation protein RutD

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_A0A377TPP8
AlphaFold — — full sequence — Viewing
ColabFold VK055_1442
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 0.872

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 24.43 0.898
2 1.15 0.009

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.

55 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
MLA
1WOM
O07015 104.1 Da LogP -0.45 TPSA 74.6 ✓ Ro5 ✓ Clean C(C(=O)O)C(=O)O
PCS
1XQX
P96084 197.7 Da LogP 1.36 TPSA 43.1 ✓ Ro5 ✓ Clean c1ccc(cc1)C[C@@H](C(=O)CCl)N
PHK
1MU0
P96084 199.7 Da LogP 1.16 TPSA 46.2 ✓ Ro5 ✓ Clean c1ccc(cc1)C[C@@H]([C@H](CCl)O)N
PMS
1WPR
O07015 172.2 Da LogP 1.07 TPSA 54.4 ✓ Ro5 ✓ Clean c1ccc(cc1)CS(=O)(=O)O
SHF
2XUA
Q13KT2 116.1 Da LogP 0.44 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)CCC(=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.