Protein profile

PA1642

selenide, water dikinase

Genome: NC_002516.2

Gene: selD PA1642 Structure source: AlphaFold UniProt Q9I383
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Amino acids 344
Annotations 7
Features 25
PDB binders 1
Druggability 0.589

Overview

Basic information about this protein and its source genome.

Accession
PA1642
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
selD PA1642
Status
annotated
Amino acids
344
Structure source
AlphaFold
EC
2.7.9.3
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0000287 Binding to a magnesium (Mg) ion. GO:0004756 Catalysis of the reaction: ATP + H2O + hydrogen selenide = AMP + 3 H+ + phosphate + selenophosphorate. GO:0016260 The chemical reactions and pathways resulting in the formation of L-selenocysteine, an essential component of glutathione peroxidase and some other proteins. GO:0070329 The substitution of a selenium atom for a sulfur atom in a ribonucleotide in a tRNA molecule.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
40.0
Human E-value
6.3e-09
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.589
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0004756 Catalysis of the reaction: ATP + H2O + hydrogen selenide = AMP + 3 H+ + phosphate + selenophosphorate.
  • GO:0016260 The chemical reactions and pathways resulting in the formation of L-selenocysteine, an essential component of glutathione peroxidase and some other proteins.
  • GO:0070329 The substitution of a selenium atom for a sulfur atom in a ribonucleotide in a tRNA molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
6 311 NCBIfam TIGR00476 selenide, water dikinase SelD
6 311 InterPro IPR004536 Selenophosphate synthetase
2 339 PANTHER PTHR10256 SELENIDE, WATER DIKINASE
2 339 InterPro IPR004536 Selenophosphate synthetase
163 339 SUPERFAMILY SSF56042 PurM C-terminal domain-like
163 339 InterPro IPR036676 PurM-like, C-terminal domain superfamily
1 344 PIRSF PIRSF036407 SelenoP_synth
1 344 InterPro IPR004536 Selenophosphate synthetase
163 343 Gene3D G3DSA:3.90.650.10 -
163 343 InterPro IPR036676 PurM-like, C-terminal domain superfamily
168 343 Pfam PF02769 AIR synthase related protein, C-terminal domain
168 343 InterPro IPR010918 PurM-like, C-terminal domain
6 158 SUPERFAMILY SSF55326 PurM N-terminal domain-like
6 158 InterPro IPR036921 PurM-like, N-terminal domain superfamily
1 161 FunFam G3DSA:3.30.1330.10:FF:000003 Selenide, water dikinase
1 161 Gene3D G3DSA:3.30.1330.10 -
1 161 InterPro IPR036921 PurM-like, N-terminal domain superfamily
7 333 CDD cd02195 SelD
7 333 InterPro IPR004536 Selenophosphate synthetase
163 344 FunFam G3DSA:3.90.650.10:FF:000004 Selenide, water dikinase
49 156 Pfam PF00586 AIR synthase related protein, N-terminal domain
49 156 InterPro IPR016188 PurM-like, N-terminal domain
1 18 ProSiteProfiles PS51257 Prokaryotic membrane lipoprotein lipid attachment site profile.
4 344 Hamap MF_00625 Selenide, water dikinase [selD].
4 344 InterPro IPR023061 Selenophosphate synthetase, class I

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA1642
AlphaFold — — full sequence — Viewing
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 0.589

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.

51 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
APC
2YYE
O67139 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.