Protein profile

KP13_13347

Uridine phosphorylase

Genome: KpKP13

Gene: udp ANJ86644.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GGL0
Amino acids 253
Annotations 10
Features 13
PDB binders 21
Druggability 0.668

Overview

Basic information about this protein and its source genome.

Accession
KP13_13347
Gene
udp ANJ86644.1
Status
annotated
Amino acids
253
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
30.435
Human E-value
3.22e-09
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
76.285
DEG E-value
3.72e-147
Localization
Cytoplasmic
ColabFold pLDDT
97.17

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 0.668
Structure A0A0H3GGL0
Pocket Pocket 4
P2Rank 0.471
Structure A0A0H3GGL0
Pocket Pocket 1
ColabFold model
FPocket 0.575 · Pocket 2
P2Rank 0.443 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 166 / 4744 genomes with a hit
Normalized 0.035

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0009166 The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
  • GO:0009116 The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0004850 Catalysis of the reaction: uridine + phosphate = uracil + alpha-D-ribose 1-phosphate.
  • 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:0016763 Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0009164 The chemical reactions and pathways resulting in the breakdown of any one of a family of organic molecules consisting of a purine or pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
  • GO:0044206 Any process which produces UMP, uridine monophosphate, from derivatives of it (e.g. cytidine, uridine, cytosine) without de novo synthesis.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
6 253 NCBIfam TIGR01718 uridine phosphorylase
6 253 InterPro IPR010058 Uridine phosphorylase
66 81 ProSitePatterns PS01232 Purine and other phosphorylases family 1 signature.
66 81 InterPro IPR018016 Nucleoside phosphorylase, conserved site
2 250 PANTHER PTHR43691 URIDINE PHOSPHORYLASE
7 250 CDD cd17767 UP_EcUdp-like
1 253 Gene3D G3DSA:3.40.50.1580 Nucleoside phosphorylase domain
1 253 InterPro IPR035994 Nucleoside phosphorylase superfamily
1 253 FunFam G3DSA:3.40.50.1580:FF:000003 Uridine phosphorylase
6 250 SUPERFAMILY SSF53167 Purine and uridine phosphorylases
6 250 InterPro IPR035994 Nucleoside phosphorylase superfamily
21 248 Pfam PF01048 Phosphorylase superfamily
21 248 InterPro IPR000845 Nucleoside phosphorylase 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_A0A0H3GGL0
AlphaFold full sequence Viewing
ColabFold KP13_13347
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
4 0.668

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 3.22 0.111
2 1.75 0.032

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.

71 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
181 P12758 294.3 Da LogP 0.65 TPSA 84.3 ✓ Ro5 ✓ Clean c1ccc(cc1)SC2=CN(C(=O)NC2=O)COCCO
182 P12758 341.2 Da LogP -1.84 TPSA 84.3 ✓ Ro5 ✓ Clean c1ccc(cc1)[Se]C2=CN(C(=O)NC2=O)COCCO
183 P12758 382.4 Da LogP 1.67 TPSA 93.6 ✓ Ro5 ✓ Clean c1ccc(cc1)COc2cccc(c2)CC3=CN(C(=O)NC3=O)COCCO
4WR Q9K4U1 202.2 Da LogP -2.04 TPSA 106.9 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1C[C@@H](CN)N)F
5UD P12758 262.2 Da LogP -2.71 TPSA 124.8 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1[C@H]2[C@@H]([C@@H]([C@H](O2)…
61N Q5E046 188.2 Da LogP 2.24 TPSA 57.5 ✓ Ro5 ✓ Clean c1cc2cc(ccc2c(c1)C(=O)O)O
6MU Q9K4U1 126.1 Da LogP 0.20 TPSA 66.2 ✓ Ro5 ✓ Clean Cc1cc(nc(n1)O)O
ANU P0A1F6 226.2 Da LogP -1.75 TPSA 93.8 ✓ Ro5 ✓ Clean C1=CN2[C@H]3[C@H]([C@@H]([C@H](O3)CO)O)OC2=NC1=O
BAU P12758 276.3 Da LogP 0.09 TPSA 84.3 ✓ Ro5 ✓ Clean c1ccc(cc1)CC2=CN(C(=O)NC2=O)COCCO
BBB P12758 398.4 Da LogP 1.38 TPSA 113.8 ✓ Ro5 ✓ Clean c1ccc(cc1)COc2cccc(c2)CC3=C(N(C(=O)NC3=O)COCCO)O
BJE Q9K4U1 226.2 Da LogP -1.75 TPSA 93.8 ✓ Ro5 ✓ Clean C1=CN2[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)OC2=NC1…
CTN Q9K4U1 243.2 Da LogP -2.56 TPSA 130.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)N=C1N)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
CYT Q9K4U1 111.1 Da LogP -0.65 TPSA 71.8 ✓ Ro5 ✓ Clean C1=C(NC(=O)N=C1)N
DUR P12758 228.2 Da LogP -1.82 TPSA 104.6 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](O[C@H]1N2C=CC(=O)NC2=O)CO)O
IMH Q2HXR2 266.3 Da LogP -2.02 TPSA 134.3 1 viol. ✓ Clean c1c(c2c([nH]1)C(=O)NC=N2)[C@H]3[C@@H]([C@@H]([C…
M5F Q9K4U1 202.2 Da LogP -2.04 TPSA 106.9 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1C[C@H](CN)N)F
TDR P0A1F6 126.1 Da LogP -0.63 TPSA 65.7 ✓ Ro5 ✓ Clean CC1=CNC(=O)NC1=O
THM P12758 242.2 Da LogP -1.51 TPSA 104.6 ✓ Ro5 ✓ Clean CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)O
URA P0A1F6 112.1 Da LogP -0.94 TPSA 65.7 ✓ Ro5 ✓ Clean C1=CNC(=O)NC1=O
URF P0A1F6 130.1 Da LogP -0.80 TPSA 65.7 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1)F
URI P0A1F6 244.2 Da LogP -2.85 TPSA 124.8 ✓ Ro5 ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…

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.