Protein profile

KP13_03029

Dethiobiotin synthetase

Genome: KpKP13

Gene: bioD AHE45586.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GLR6
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Amino acids 240
Annotations 4
Features 15
PDB binders 9
Druggability 0.758

Overview

Basic information about this protein and its source genome.

Accession
KP13_03029
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
bioD AHE45586.1
Status
annotated
Amino acids
240
Structure source
AlphaFold + ColabFold
GO
GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0009102 The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid. GO:0000287 Binding to a magnesium (Mg) ion. GO:0004141 Catalysis of the reaction: 7,8-diaminononanoate + ATP + CO2 = ADP + dethiobiotin + 4 H+ + phosphate.

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 (%)
52.252
DEG E-value
2.0900000000000001e-57
Localization
Cytoplasmic
ColabFold pLDDT
94.27

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 0.758
Structure A0A0H3GLR6
Pocket Pocket 6
P2Rank 0.825
Structure A0A0H3GLR6
Pocket Pocket 1
ColabFold model
FPocket 0.51 · Pocket 5
P2Rank 0.678 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 114 / 4744 genomes with a hit
Normalized 0.024

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0009102 The chemical reactions and pathways resulting in the formation of biotin, cis-tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0004141 Catalysis of the reaction: 7,8-diaminononanoate + ATP + CO2 = ADP + dethiobiotin + 4 H+ + phosphate.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
1 228 PIRSF PIRSF006755 DTB_synth
1 228 InterPro IPR004472 Dethiobiotin synthase BioD
3 193 CDD cd03109 DTBS
6 176 NCBIfam TIGR00347 dethiobiotin synthase
6 176 InterPro IPR004472 Dethiobiotin synthase BioD
1 211 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
1 211 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
2 225 Gene3D G3DSA:3.40.50.300 -
2 225 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
3 225 FunFam G3DSA:3.40.50.300:FF:000292 ATP-dependent dethiobiotin synthetase BioD
3 211 Pfam PF13500 AAA domain
2 212 Hamap MF_00336 ATP-dependent dethiobiotin synthetase BioD [bioD].
2 212 InterPro IPR004472 Dethiobiotin synthase BioD
1 224 PANTHER PTHR43210 DETHIOBIOTIN SYNTHETASE
1 224 InterPro IPR004472 Dethiobiotin synthase BioD

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_A0A0H3GLR6
AlphaFold — — full sequence — Viewing
ColabFold KP13_03029
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 0.758

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 8.35 0.445
2 1.03 0.006

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.