Protein profile

VK055_1732

adenosylmethionine-8-amino-7-oxononanoate transaminase

Genome: KpATCC43816

Gene: bioA AIK80352.1 Structure source: Experimental + ColabFold UniProt A0A422Z2E3
Amino acids 410
Annotations 7
Features 17
PDB binders 26
Druggability 0.536

Overview

Basic information about this protein and its source genome.

Accession
VK055_1732
Gene
bioA AIK80352.1
Status
annotated
Amino acids
410
Structure source
Experimental + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
29.469
Human E-value
1.5199999999999996e-34
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
57.921
DEG E-value
4.8799999999999995e-174
Localization
Cytoplasmic
ColabFold pLDDT
98.29

Selected Druggability evidence

PDB experimental structure

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 0.536
Structure 7UG3
Pocket Pocket 2
P2Rank 0.312
Structure 7UG3
Pocket Pocket 1
ColabFold model
FPocket 0.503 · Pocket 1
P2Rank 0.631 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 540 / 4744 genomes with a hit
Normalized 0.114

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: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:0004015 Catalysis of the reaction: (8S)-8-amino-7-oxononanoate + S-adenosyl-L-methionine = S-adenosyl-4-methylsulfanyl-2-oxobutanoate + (7R,8S)-7,8-diammoniononanoate.
  • 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:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
4 403 PANTHER PTHR42684 ADENOSYLMETHIONINE-8-AMINO-7-OXONONANOATE AMINOTRANSFERASE
1 402 NCBIfam TIGR00508 adenosylmethionine--8-amino-7-oxononanoate transaminase
1 402 InterPro IPR005815 Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA
223 260 ProSitePatterns PS00600 Aminotransferases class-III pyridoxal-phosphate attachment site.
223 260 InterPro IPR005814 Aminotransferase class-III
42 311 Gene3D G3DSA:3.40.640.10 -
42 311 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
42 311 FunFam G3DSA:3.40.640.10:FF:000041 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
1 402 CDD cd00610 OAT_like
1 402 InterPro IPR005814 Aminotransferase class-III
1 397 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
1 397 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
1 402 Hamap MF_00834 Adenosylmethionine-8-amino-7-oxononanoate aminotransferase [bioA].
8 401 Pfam PF00202 Aminotransferase class-III
8 401 InterPro IPR005814 Aminotransferase class-III
5 403 SUPERFAMILY SSF53383 PLP-dependent transferases
5 403 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.

3D visualization script Full viewer

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Structural evidence

1 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 7UG3
X-ray 1.90 Å A,B,C,D
100.0% 1-410
Viewing
ColabFold VK055_1732
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
59 0.522
54 0.255
5 0.242

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 11.25 0.602
2 9.66 0.519
3 8.55 0.457
4 7.6 0.401
5 6.71 0.342

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.

176 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
2B1 P9WQ81 394.3 Da LogP 3.60 TPSA 137.5 ✓ Ro5 Alert Cc1c(c(c(cn1)COP(=O)(O)O)C/N=N/c2nc3ccccc3s2)O
2B6 P9WQ81 422.4 Da LogP 3.11 TPSA 154.6 ✓ Ro5 Alert Cc1c(c(c(cn1)COP(=O)(O)O)C/N=N/C(=O)c2nc3ccccc3…
2B9 P9WQ81 366.3 Da LogP 1.94 TPSA 153.7 ✓ Ro5 Alert CC1=C(/C(=C\N=N\C(=O)c2ccncc2)/C(=CN1)COP(=O)(O…
2BG P9WQ81 164.2 Da LogP 1.75 TPSA 38.9 ✓ Ro5 ✓ Clean c1ccc2c(c1)nc(s2)CN
3G9 P9WQ80 342.8 Da LogP 3.51 TPSA 40.6 ✓ Ro5 ✓ Clean CC(=O)c1ccc(cc1)N2CCN(CC2)C(=O)c3cccc(c3)Cl
3GS P9WQ80 351.4 Da LogP 2.09 TPSA 74.6 ✓ Ro5 ✓ Clean COC(=O)c1c2n(c(c1C(=O)OC)c3cccc(c3)F)C[S@](=O)C2
3VQ P9WQ81 204.3 Da LogP 1.91 TPSA 56.0 ✓ Ro5 ✓ Clean c1ccnc(c1)c2ccc(s2)C(=O)N
3VR P9WQ81 201.3 Da LogP 1.65 TPSA 29.9 ✓ Ro5 ✓ Clean CNCc1ccc(cc1)Cn2cccn2
3VS P9WQ81 187.2 Da LogP 0.97 TPSA 60.9 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)N)n2ccnc2
3VW P9WQ81 189.3 Da LogP 1.87 TPSA 29.1 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)C2CCNCC2
3VX P9WQ81 187.2 Da LogP 1.85 TPSA 46.2 ✓ Ro5 ✓ Clean CC(=O)Nc1ccc2c(c1)C=CC2=O
3W1 P9WQ81 221.7 Da LogP 2.04 TPSA 43.8 ✓ Ro5 ✓ Clean c1cc(ccc1CN)Cn2cc(cn2)Cl
40N P9WQ81 283.3 Da LogP 3.06 TPSA 51.3 ✓ Ro5 ✓ Clean c1ccc(c(c1)C2=CC(=O)c3cc4c(cc3N2)OCO4)F
41E P9WQ81 414.5 Da LogP 4.23 TPSA 75.7 ✓ Ro5 ✓ Clean CC(=O)c1ccc(s1)C(=O)N2CCC(CC2)CCC(=O)Nc3cccc(c3…
41F P9WQ81 339.4 Da LogP 3.05 TPSA 61.4 ✓ Ro5 ✓ Clean c1ccc(cc1)N2CCN(CC2)C(=O)Nc3ccc4c(c3)nns4
41N P9WQ81 352.4 Da LogP 2.58 TPSA 59.1 ✓ Ro5 ✓ Clean CC(=O)c1ccc(cc1)N2CCN(CC2)C(=O)c3ccc4c(c3)OCO4
41O P9WQ81 352.8 Da LogP 3.51 TPSA 40.6 ✓ Ro5 ✓ Clean c1cc(cc(c1)Cl)C(=O)N2CCN(CC2)c3ccc4c(c3)C=CC4=O
6SQ P0A4X7 341.8 Da LogP 4.64 TPSA 37.4 ✓ Ro5 ✓ Clean CC(=O)c1ccc(cc1)N2CCC(CC2)C(=O)c3cccc(c3)Cl
6SR P0A4X7 364.4 Da LogP 2.51 TPSA 59.1 ✓ Ro5 ✓ Clean c1cc2c(cc1C(=O)N3CCN(CC3)c4ccc5c(c4)CCC5=O)OCO2
7B9 P0A4X7 399.3 Da LogP 0.93 TPSA 165.0 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=CNC(=CC2=O)CCCO)O
ACZ P12995 196.2 Da LogP 0.25 TPSA 89.3 ✓ Ro5 ✓ Clean C1=CC(C=CC1CC[C@@H](C(=O)O)N)N
FOR P9WQ81 30.0 Da LogP -0.18 TPSA 17.1 ✓ Ro5 ✓ Clean C=O
J4J P12995 227.2 Da LogP 0.68 TPSA 98.3 ✓ Ro5 ✓ Clean c1ccc(c(c1)[N+](=O)[O-])SCC(=O)NN
KAP P9WQ81 187.2 Da LogP 0.94 TPSA 80.4 ✓ Ro5 ✓ Clean C[C@@H](C(=O)CCCCCC(=O)O)N
PL8 P9WQ81 399.3 Da LogP 0.93 TPSA 165.0 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=CC=C(NC2=O)CCCO)O
TAR D2TPI3 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@H]([C@@H](C(=O)O)O)(C(=O)O)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.