Protein profile

KP13_02015

Thymidine phosphorylase

Genome: KpKP13

Gene: AHE46452.1 deoA Structure source: AlphaFold + ColabFold UniProt A0A0H3GRD1
Amino acids 440
Annotations 10
Features 32
PDB binders 7
Druggability 0.835

Overview

Basic information about this protein and its source genome.

Accession
KP13_02015
Gene
AHE46452.1 deoA
Status
annotated
Amino acids
440
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
51.852
Human E-value
8.49e-09
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.24

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 0.835
Structure A0A0H3GRD1
Pocket Pocket 4
P2Rank 0.915
Structure A0A0H3GRD1
Pocket Pocket 1
ColabFold model
FPocket 0.558 · Pocket 3
P2Rank 0.869 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 155 / 4744 genomes with a hit
Normalized 0.033

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:0006206 The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
  • GO:0009032 Catalysis of the reaction: thymidine + phosphate = thymine + 2-deoxy-D-ribose 1-phosphate.
  • GO:0016757 Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
  • GO:0004645 Catalysis of the reaction: 1,4-alpha-D-glucosyl(n) + phosphate = 1,4-alpha-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate.
  • GO:0006213 The chemical reactions and pathways involving any pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
  • GO:0016763 Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
  • GO:0016154 Catalysis of the reaction: pyrimidine nucleoside + phosphate = pyrimidine + alpha-D-ribose 1-phosphate.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0046104 The chemical reactions and pathways involving thymidine, deoxyribosylthymine thymine 2-deoxyriboside, a deoxynucleoside very widely distributed but occurring almost entirely as phosphoric esters in deoxynucleotides and deoxyribonucleic acid, DNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
350 424 SMART SM00941 PYNP_C_2
350 424 InterPro IPR013102 Pyrimidine nucleoside phosphorylase, C-terminal
70 335 FunFam G3DSA:3.40.1030.10:FF:000001 Thymidine phosphorylase
74 334 SUPERFAMILY SSF52418 Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
74 334 InterPro IPR035902 Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily
6 67 Pfam PF02885 Glycosyl transferase family, helical bundle domain
6 67 InterPro IPR017459 Glycosyl transferase family 3, N-terminal domain
5 423 NCBIfam TIGR02644 pyrimidine-nucleoside phosphorylase
5 423 InterPro IPR018090 Pyrimidine-nucleoside phosphorylase, bacterial/eukaryotic
337 433 Gene3D G3DSA:3.90.1170.30 -
337 433 InterPro IPR036566 Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily
2 438 NCBIfam TIGR02643 thymidine phosphorylase
2 438 InterPro IPR013465 Thymidine phosphorylase
350 423 Pfam PF07831 Pyrimidine nucleoside phosphorylase C-terminal domain
350 423 InterPro IPR013102 Pyrimidine nucleoside phosphorylase, C-terminal
337 439 SUPERFAMILY SSF54680 Pyrimidine nucleoside phosphorylase C-terminal domain
337 439 InterPro IPR036566 Pyrimidine nucleoside phosphorylase-like, C-terminal domain superfamily
79 309 Pfam PF00591 Glycosyl transferase family, a/b domain
79 309 InterPro IPR000312 Glycosyl transferase, family 3
70 325 Gene3D G3DSA:3.40.1030.10 Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain
70 325 InterPro IPR035902 Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain superfamily
3 439 PANTHER PTHR10515 THYMIDINE PHOSPHORYLASE
3 439 InterPro IPR000053 Thymidine/pyrimidine-nucleoside phosphorylase
6 194 Gene3D G3DSA:1.20.970.10 Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C
337 433 FunFam G3DSA:3.90.1170.30:FF:000001 Thymidine phosphorylase
2 70 SUPERFAMILY SSF47648 Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain
2 70 InterPro IPR036320 Glycosyl transferase family 3, N-terminal domain superfamily
1 439 PIRSF PIRSF000478 TP_PyNP
1 439 InterPro IPR000053 Thymidine/pyrimidine-nucleoside phosphorylase
113 128 ProSitePatterns PS00647 Thymidine and pyrimidine-nucleoside phosphorylases signature.
113 128 InterPro IPR017872 Pyrimidine-nucleoside phosphorylase, conserved site
2 438 Hamap MF_01628 Thymidine phosphorylase [deoA].

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_A0A0H3GRD1
AlphaFold full sequence Viewing
ColabFold KP13_02015
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 0.835

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 19.98 0.848
2 4.72 0.207

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
0NP P07650 272.2 Da LogP -1.32 TPSA 134.6 ✓ Ro5 Alert C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…
AZZ P07650 267.2 Da LogP -0.20 TPSA 133.1 ✓ Ro5 Alert CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)CO)N=[…
CTN Q7CP66 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…
IUR P19971 238.0 Da LogP -0.33 TPSA 65.7 ✓ Ro5 ✓ Clean C1=C(C(=O)NC(=O)N1)I
THM Q7CP66 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 P77836 112.1 Da LogP -0.94 TPSA 65.7 ✓ Ro5 ✓ Clean C1=CNC(=O)NC1=O
URI Q7CP66 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.