Protein profile

KP13_02013

Purine nucleoside phosphorylase deoD-type

Genome: KpKP13

Gene: deoD AHE46450.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GM89
Amino acids 239
Annotations 9
Features 16
PDB binders 26
Druggability 0.684

Overview

Basic information about this protein and its source genome.

Accession
KP13_02013
Gene
deoD AHE46450.1
Status
annotated
Amino acids
239
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
44.589
DEG E-value
7.28e-61
Localization
Cytoplasmic
ColabFold pLDDT
97.12

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 0.684
Structure A0A0H3GM89
Pocket Pocket 6
P2Rank 0.797
Structure A0A0H3GM89
Pocket Pocket 1
ColabFold model
FPocket 0.899 · Pocket 1
P2Rank 0.795 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 877 / 4744 genomes with a hit
Normalized 0.185

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • 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:0004731 Catalysis of the reaction: purine nucleoside + phosphate = purine + 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:0006139 Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
  • 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:0047975 Catalysis of the reaction: guanosine + phosphate = alpha-D-ribose 1-phosphate + guanine.
  • GO:0006152 The chemical reactions and pathways resulting in the breakdown of purine nucleoside, one of a family of organic molecules consisting of a purine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
5 234 NCBIfam TIGR00107 purine-nucleoside phosphorylase
5 234 InterPro IPR004402 Purine nucleoside phosphorylase DeoD-type
5 232 CDD cd09006 PNP_EcPNPI-like
5 232 InterPro IPR004402 Purine nucleoside phosphorylase DeoD-type
62 77 ProSitePatterns PS01232 Purine and other phosphorylases family 1 signature.
62 77 InterPro IPR018016 Nucleoside phosphorylase, conserved site
15 220 Pfam PF01048 Phosphorylase superfamily
15 220 InterPro IPR000845 Nucleoside phosphorylase domain
3 234 SUPERFAMILY SSF53167 Purine and uridine phosphorylases
3 234 InterPro IPR035994 Nucleoside phosphorylase superfamily
2 235 Hamap MF_01627 Purine nucleoside phosphorylase DeoD-type [deoD].
2 235 InterPro IPR004402 Purine nucleoside phosphorylase DeoD-type
1 238 Gene3D G3DSA:3.40.50.1580 Nucleoside phosphorylase domain
1 238 InterPro IPR035994 Nucleoside phosphorylase superfamily
1 235 FunFam G3DSA:3.40.50.1580:FF:000002 Purine nucleoside phosphorylase DeoD-type
4 232 PANTHER PTHR43691 URIDINE PHOSPHORYLASE

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_A0A0H3GM89
AlphaFold full sequence Viewing
ColabFold KP13_02013
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
6 0.684

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 9.22 0.494
2 5.6 0.269

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.

76 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
223 A2E7Y6 263.3 Da LogP -0.67 TPSA 111.3 ✓ Ro5 ✓ Clean c1c(c2c([nH]1)c(ncn2)N)C[N@@]3C[C@@H]([C@H](C3)…
2FA P0ABP9 285.2 Da LogP -1.84 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc2c(nc(nc2n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)…
2FD P0ABP9 269.2 Da LogP -0.81 TPSA 119.3 ✓ Ro5 ✓ Clean c1nc2c(nc(nc2n1[C@H]3C[C@@H]([C@H](O3)CO)O)F)N
6CR O34925 301.7 Da LogP -1.33 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)nc…
6MP P0ABP8 134.1 Da LogP 0.66 TPSA 54.5 ✓ Ro5 ✓ Clean Cc1c2c(nc[nH]2)ncn1
7HX P0ABP8 135.1 Da LogP 0.66 TPSA 61.8 ✓ Ro5 ✓ Clean c1c[nH]c2c1c(ncn2)O
AC2 A7ZVS7 225.2 Da LogP -1.33 TPSA 119.0 ✓ Ro5 ✓ Clean c1nc2c(n1COCCO)N=C(NC2=O)N
ADE O34925 135.1 Da LogP -0.06 TPSA 80.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(ncn2)N
ADN P0ABP9 267.2 Da LogP -1.98 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BG2 O34925 362.1 Da LogP -1.92 TPSA 159.5 ✓ Ro5 ✓ Clean C([C@@H]1[C@H]([C@H]([C@@H](O1)n2c3c(nc2Br)C(=O…
DBM P0ABP8 280.3 Da LogP -0.87 TPSA 113.5 ✓ Ro5 ✓ Clean Cc1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DIH B1JL34 265.3 Da LogP -2.38 TPSA 106.4 ✓ Ro5 ✓ Clean c1c(c2c([nH]1)C(=O)NC=N2)C[NH+]3C[C@@H]([C@H](C…
FM1 P0ABP8 281.3 Da LogP -1.45 TPSA 136.4 ✓ Ro5 ✓ Clean CNc1c2c(c(n[nH]2)[C@H]3[C@@H]([C@@H]([C@H](O3)C…
FM2 P0ABP8 282.3 Da LogP -2.48 TPSA 141.4 ✓ Ro5 ✓ Clean C[n+]1cnc2c(c1N)[nH]nc2[C@H]3[C@@H]([C@@H]([C@H…
FMB P0ABP8 268.2 Da LogP -2.20 TPSA 144.4 ✓ Ro5 ✓ Clean C1=Nc2c(n[nH]c2C(=O)N1)[C@H]3[C@@H]([C@@H]([C@H…
FMC P0ABP8 267.2 Da LogP -1.91 TPSA 150.4 ✓ Ro5 ✓ Clean c1nc2c(c(n1)N)[nH]nc2[C@H]3[C@@H]([C@@H]([C@H](…
GA2 O34925 255.2 Da LogP -1.97 TPSA 139.3 ✓ Ro5 ✓ Clean c1nc2c(n1COC(CO)CO)N=C(NC2=O)N
HPA P56463 136.1 Da LogP -0.35 TPSA 74.4 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)N=CNC2=O
MDR P0ABP8 250.3 Da LogP -0.22 TPSA 93.3 ✓ Ro5 ✓ Clean Cc1c2c(ncn1)n(cn2)[C@H]3C[C@@H]([C@H](O3)CO)O
MTP P0ABP9 298.3 Da LogP -0.84 TPSA 113.5 ✓ Ro5 ✓ Clean CSc1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3…
NOS P0ABP9 268.2 Da LogP -2.27 TPSA 133.5 ✓ Ro5 ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO)O)O)N=…
RAB P0ABP9 267.2 Da LogP -1.98 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@H]([C@@H]([C@H](O3)C…
TAL P0ABP8 280.3 Da LogP -0.87 TPSA 113.5 ✓ Ro5 ✓ Clean Cc1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
TBN P0ABP9 266.3 Da LogP -1.38 TPSA 126.7 ✓ Ro5 ✓ Clean c1cn(c2c1c(ncn2)N)[C@H]3[C@@H]([C@@H]([C@H](O3)…
UA2 A2E7Y6 265.3 Da LogP -1.73 TPSA 140.3 1 viol. ✓ Clean c1c(c2c([nH]1)c(ncn2)N)[C@H]3[C@@H]([C@@H]([C@H…
XYA P0ABP9 267.2 Da LogP -1.98 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]([C@H](O3)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.