Protein profile

PA0501

8-amino-7-oxononanoate synthase

Genome: NC_002516.2

Gene: PA0501 bioF Structure source: AlphaFold UniProt Q9I617
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Amino acids 401
Annotations 7
Features 16
PDB binders 9
Druggability 0.727

Overview

Basic information about this protein and its source genome.

Accession
PA0501
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA0501 bioF
Status
annotated
Amino acids
401
Structure source
AlphaFold
EC
2.3.1.47
GO
GO:0008710 Catalysis of the reaction: L-alanine + H+ + pimelyl-CoA = 8-amino-7-oxononanoate + CO2 + CoA. GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6. 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:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2. GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
42.105
Human E-value
2.35e-12
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 0.727
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MSFDLASRLASRRAEDLYRQRPLLESAQGPDVVVDGQPLLAFCSNDYLGLANHPEVIAALRAGAERWGVGGGASHLVVGHSGPHHELELALAEFTGRPRALLFSTGYMANLGAVAALVGKGDTVLEDRLNHASLLDAGLLSGARFSRYLHNDPASLAARLDKAEGNTLVVTDGVFSMDGNLADLPALAAVAQARGAWLMVDDAHGFGPLGASGGGIVEHFGLGQEQVPVLIGTLGKGFGTAGAFVAGSEELIETLIQYARPYIYTTSQPPAVACATLKSLELLRRESWRRQHLAALIARFRHGAEALGLTLMDSFTPIQPILVGGSRQAVALAGMLRARGIMVGAIRPPTVPANSARLRVTLSAAHSEAQVDRLLEALGESWRQLSSSLLAEIEAEEGDDA

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:0008710 Catalysis of the reaction: L-alanine + H+ + pimelyl-CoA = 8-amino-7-oxononanoate + CO2 + CoA.
  • GO:0030170 Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
  • 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:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • GO:0009058 A cellular process consisting of the biochemical pathways by which a living organism synthesizes chemical substances. This typically represents the energy-requiring part of metabolism in which simpler substances are transformed into more complex ones.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
17 378 NCBIfam TIGR00858 8-amino-7-oxononanoate synthase
17 378 InterPro IPR004723 8-amino-7-oxononanoate synthase, Archaea/Proteobacteria type
55 284 Gene3D G3DSA:3.40.640.10 -
55 284 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
22 378 PANTHER PTHR13693 CLASS II AMINOTRANSFERASE/8-AMINO-7-OXONONANOATE SYNTHASE
39 376 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
39 376 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
39 378 Pfam PF00155 Aminotransferase class I and II
39 378 InterPro IPR004839 Aminotransferase, class I/classII
233 242 ProSitePatterns PS00599 Aminotransferases class-II pyridoxal-phosphate attachment site.
233 242 InterPro IPR001917 Aminotransferase, class-II, pyridoxal-phosphate binding site
1 382 Hamap MF_01693 8-amino-7-oxononanoate synthase [bioF].
1 382 InterPro IPR022834 8-amino-7-oxononanoate synthase, Proteobacteria
37 382 CDD cd06454 KBL_like
6 385 SUPERFAMILY SSF53383 PLP-dependent transferases
6 385 InterPro IPR015424 Pyridoxal phosphate-dependent transferase

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 PA0501
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
5 0.679
4 0.672
10 0.243
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.

40 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
2BK
7BXQ
Q0K313 350.3 Da LogP -0.37 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H]([C@H](C)O)C(=…
AKB
1FC4
P0AB77 117.1 Da LogP -1.01 TPSA 80.4 ✓ Ro5 ✓ Clean CC(=O)[C@@H](C(=O)O)N
BEN
5VNX
A9AE46 120.2 Da LogP 0.97 TPSA 49.9 ✓ Ro5 ✓ Clean [H]/N=C(\c1ccccc1)/N
F9X
7BXR
Q0K313 364.3 Da LogP 0.02 TPSA 169.4 1 viol. ✓ Clean CC[C@H]([C@@H](C(=O)O)NCc1c(cnc(c1O)C)COP(=O)(O…
KAM
1DJ9
P12998 418.4 Da LogP 1.79 TPSA 166.3 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](C)C(=O)CCCCCC…
LLF
2G6W
P12998 310.2 Da LogP 1.39 TPSA 112.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)C=NCC(F)F)O
PLG
7BXS
Q0K313 306.2 Da LogP -0.12 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNCC(=O)O)O
PLS
2W8J
Q93UV0 336.2 Da LogP -0.76 TPSA 169.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CO)C(=O)O)O
PMP
2XBN
Q93UV0 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O

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.