Protein profile

PA0504

ATP-dependent dethiobiotin synthetase BioD

Genome: NC_002516.2

Gene: PA0504 bioD Structure source: AlphaFold UniProt Q9I614
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Amino acids 228
Annotations 7
Features 15
PDB binders 9
Druggability 0.848

Overview

Basic information about this protein and its source genome.

Accession
PA0504
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA0504 bioD
Status
annotated
Amino acids
228
Structure source
AlphaFold
EC
6.3.3.3
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0004141 Catalysis of the reaction: 7,8-diaminononanoate + ATP + CO2 = ADP + dethiobiotin + 4 H+ + phosphate. GO:0000287 Binding to a magnesium (Mg) ion. GO:0042803 Binding to an identical protein to form a homodimer. GO:0009102 The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
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 0.848
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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004141 Catalysis of the reaction: 7,8-diaminononanoate + ATP + CO2 = ADP + dethiobiotin + 4 H+ + phosphate.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0042803 Binding to an identical protein to form a homodimer.
  • GO:0009102 The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
1 214 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
1 214 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 226 PIRSF PIRSF006755 DTB_synth
1 226 InterPro IPR004472 Dethiobiotin synthase BioD
3 222 Gene3D G3DSA:3.40.50.300 -
3 222 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
2 224 FunFam G3DSA:3.40.50.300:FF:000292 ATP-dependent dethiobiotin synthetase BioD
4 212 Pfam PF13500 AAA domain
1 218 Hamap MF_00336 ATP-dependent dethiobiotin synthetase BioD [bioD].
1 218 InterPro IPR004472 Dethiobiotin synthase BioD
5 176 NCBIfam TIGR00347 dethiobiotin synthase
5 176 InterPro IPR004472 Dethiobiotin synthase BioD
1 217 PANTHER PTHR43210 DETHIOBIOTIN SYNTHETASE
1 217 InterPro IPR004472 Dethiobiotin synthase BioD
2 194 CDD cd03109 DTBS

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 + 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 PA0504
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
6 0.848
1 0.213

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.

59 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
8AC
3MLE
O24872 159.2 Da LogP 1.37 TPSA 63.3 ✓ Ro5 ✓ Clean C(CCCC(=O)O)CCCN
ACP
1DAG
P13000 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)…
ANP
3QXS
O24872 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
DAA
1BS1
P13000 315.2 Da LogP 1.81 TPSA 101.7 ✓ Ro5 ✓ Clean C[C@@H]([C@@H](CCCCCC(=O)O)NC(=O)O[Al-](F)(F)F)N
DNN
1A82
P13000 188.3 Da LogP 0.70 TPSA 89.3 ✓ Ro5 ✓ Clean C[C@@H]([C@@H](CCCCCC(=O)O)N)N
DPU
1DAK
P13000 312.3 Da LogP 0.56 TPSA 159.2 ✓ Ro5 ✓ Clean C[C@@H]([C@@H](CCCCCC(=O)O)NC(=O)OP(=O)(O)O)N
DSD
1DAF
P13000 232.3 Da LogP 1.00 TPSA 112.7 ✓ Ro5 ✓ Clean C[C@@H]([C@@H](CCCCCC(=O)O)NC(=O)O)N
DTB
1DAM
P13000 214.3 Da LogP 1.09 TPSA 78.4 ✓ Ro5 ✓ Clean C[C@H]1[C@H](NC(=O)N1)CCCCCC(=O)O
IKT
1DAE
P13000 231.3 Da LogP 1.46 TPSA 100.6 ✓ Ro5 ✓ Clean C[C@@H]([C@@H](CCCCCC(=O)O)CC(=O)O)N

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.