Protein profile

PA0500

biotin synthase

Genome: NC_002516.2

Gene: bioB PA0500 Structure source: AlphaFold UniProt Q9I618
Export view
Amino acids 352
Annotations 8
Features 26
PDB binders 15
Druggability 0.816

Overview

Basic information about this protein and its source genome.

Accession
PA0500
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
bioB PA0500
Status
annotated
Amino acids
352
Structure source
AlphaFold
EC
2.8.1.6
GO
GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands. GO:0004076 Catalysis of the reaction: (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = [sulfur carrier]-H + biotin + 2 5'-deoxyadenosine + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin]. GO:0005506 Binding to an iron (Fe) ion. 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: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.

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 0.816
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0051537 Binding to a 2 iron, 2 sulfur (2Fe-2S) cluster; this cluster consists of two iron atoms, with two inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0004076 Catalysis of the reaction: (4R,5S)-dethiobiotin + [sulfur carrier]-SH + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = [sulfur carrier]-H + biotin + 2 5'-deoxyadenosine + 2 L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin].
  • GO:0005506 Binding to an iron (Fe) ion.
  • 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: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:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.

Sequence Features

Domain/signature hits from InterPro and related databases.

26 records
Show feature table
Start End DB Term Name
56 208 Pfam PF04055 Radical SAM superfamily
56 208 InterPro IPR007197 Radical SAM
12 316 NCBIfam TIGR00433 biotin synthase BioB
12 316 InterPro IPR002684 Biotin synthase/Biotin biosynthesis bifunctional protein BioAB
10 321 FunFam G3DSA:3.20.20.70:FF:000011 Biotin synthase
226 316 Pfam PF06968 Biotin and Thiamin Synthesis associated domain
226 316 InterPro IPR010722 Biotin and thiamin synthesis-associated domain
4 325 SFLD SFLDG01278 biotin synthase like
5 333 PANTHER PTHR22976 BIOTIN SYNTHASE
5 333 InterPro IPR002684 Biotin synthase/Biotin biosynthesis bifunctional protein BioAB
226 318 SMART SM00876 BATS_2
226 318 InterPro IPR010722 Biotin and thiamin synthesis-associated domain
49 261 SMART SM00729 MiaB
49 261 InterPro IPR006638 Elp3/MiaA/NifB-like, radical SAM core domain
56 255 CDD cd01335 Radical_SAM
10 321 Gene3D G3DSA:3.20.20.70 Aldolase class I
10 321 InterPro IPR013785 Aldolase-type TIM barrel
4 325 SFLD SFLDF00272 biotin synthase
4 325 InterPro IPR024177 Biotin synthase
11 319 Hamap MF_01694 Biotin synthase [bioB].
11 319 InterPro IPR002684 Biotin synthase/Biotin biosynthesis bifunctional protein BioAB
11 320 SUPERFAMILY SSF102114 Radical SAM enzymes
1 325 PIRSF PIRSF001619 Biotin_synth
1 325 InterPro IPR024177 Biotin synthase
44 262 ProSiteProfiles PS51918 Radical SAM core domain profile.
44 262 InterPro IPR007197 Radical SAM

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

Loading 3D structure...

Legend High Medium Low

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 PA0500
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 0.816

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.

65 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
1N7
4JXC
Q9X0Z6 631.9 Da LogP 2.20 TPSA 164.4 2 viol. ✓ Clean C[C@H](CCC(=O)NCCC[N+](C)(C)CC(CS(=O)(=O)O)O)[C…
41K
5FEP
Q9X0Z6 191.2 Da LogP -0.42 TPSA 86.6 ✓ Ro5 ✓ Clean C[C@]1(N[C@@H](CS1)C(=O)O)C(=O)O
5AD
3IIX
Q9X0Z6 251.2 Da LogP -0.95 TPSA 119.3 ✓ Ro5 ✓ Clean C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)O)O
5X8
5FEW
Q9X0Z6 370.4 Da LogP -1.83 TPSA 182.6 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
5XB
5FF2
Q9X0Z6 177.2 Da LogP -0.81 TPSA 86.6 ✓ Ro5 ✓ Clean C1[C@H](N[C@H](S1)C(=O)O)C(=O)O
5ZZ
5FF4
Q9X0Z6 219.3 Da LogP 0.36 TPSA 86.6 ✓ Ro5 ✓ Clean C[C@]1(N[C@@H](C(S1)(C)C)C(=O)O)C(=O)O
9SE
5FES
Q9X0Z6 238.1 Da LogP -1.03 TPSA 86.6 ✓ Ro5 ✓ Clean C[C@]1(N[C@@H](C[Se]1)C(=O)O)C(=O)O
CPS
3CIW
Q9X0Z6 614.9 Da LogP 2.88 TPSA 147.0 1 viol. ✓ Clean C[C@H](CCC(=O)NCCC[N+](C)(C)CCCS(=O)(=O)[O-])[C…
DTB
1R30
P12996 214.3 Da LogP 1.09 TPSA 78.4 ✓ Ro5 ✓ Clean C[C@H]1[C@H](NC(=O)N1)CCCCCC(=O)O
FES
1R30
P12996 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
PRS
5FF3
Q9X0Z6 133.2 Da LogP -0.27 TPSA 49.3 ✓ Ro5 ✓ Clean C1[C@H](NCS1)C(=O)O
SAT
3CIW
Q9X0Z6 140.1 Da LogP -1.04 TPSA 91.7 ✓ Ro5 ✓ Clean C(C(=O)O)S(=O)(=O)O
SE
5FF4
Q9X0Z6 81.0 Da LogP -0.92 TPSA 0.0 ✓ Ro5 ✓ Clean [SeH2]
SEC
5FEX
Q9X0Z6 168.1 Da LogP -1.28 TPSA 63.3 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)N)[SeH]
SFS
5FF4
Q9X0Z6 539.2 Da LogP -1.53 TPSA 0.0 1 viol. ✓ Clean [Fe]12[Se]3[Fe]4[Se]1[Fe]5[Se]2[Fe]3[Se]45

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.