Protein target profile

VK055_1732

adenosylmethionine-8-amino-7-oxononanoate transaminase

Genome: KpATCC43816 Gene: AIK80352.1 bioA 3D evidence: Experimental + ColabFold model Metabolism 1 reaction UniProt A0A422Z2E3
Length 410
Pocket druggability 0.536
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 176 total records
Functional annotation 1 EC 6 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
Hit
Human identity (%)
29.469 Lower values reduce human off-target concern.
Human E-value
1.5199999999999996e-34
Gut microbiome similarity
11.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
57.921 Higher values support similarity to known essential genes.
DEG E-value
4.8799999999999995e-174 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
98.29 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so 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
Prevalence 11.4%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Structure

Chemistry

ChEMBL 3G8 ChEMBL CHEMBL1200545 ChEMBL CHEMBL1201139 ChEMBL CHEMBL1299213 ChEMBL CHEMBL1301524 ChEMBL CHEMBL1302669 ChEMBL CHEMBL1303050 ChEMBL CHEMBL1305572 ChEMBL CHEMBL1306386 ChEMBL CHEMBL1307243 ChEMBL CHEMBL1307837 ChEMBL CHEMBL1308221 ChEMBL CHEMBL1310068 ChEMBL CHEMBL1312255 ChEMBL CHEMBL1319207 ChEMBL CHEMBL1320489 ChEMBL CHEMBL1323069 ChEMBL CHEMBL1324067 ChEMBL CHEMBL1324387 ChEMBL CHEMBL1326515 ChEMBL CHEMBL1330095 ChEMBL CHEMBL1331390 ChEMBL CHEMBL1333563 ChEMBL CHEMBL1335585 ChEMBL CHEMBL1336898 ChEMBL CHEMBL1338128 ChEMBL CHEMBL1338285 ChEMBL CHEMBL1340866 ChEMBL CHEMBL1340904 ChEMBL CHEMBL1342451 ChEMBL CHEMBL1342774 ChEMBL CHEMBL1343310 ChEMBL CHEMBL1344564 ChEMBL CHEMBL1345665 ChEMBL CHEMBL1346733 ChEMBL CHEMBL1348250 ChEMBL CHEMBL1350707 ChEMBL CHEMBL1350829 ChEMBL CHEMBL1359708 ChEMBL CHEMBL1360391 ChEMBL CHEMBL1362037 ChEMBL CHEMBL1363639 ChEMBL CHEMBL1368850 ChEMBL CHEMBL1370314 ChEMBL CHEMBL1372754 ChEMBL CHEMBL1374181 ChEMBL CHEMBL1374473 ChEMBL CHEMBL1375691 ChEMBL CHEMBL1380624 ChEMBL CHEMBL1381449 ChEMBL CHEMBL1382858 ChEMBL CHEMBL1383792 ChEMBL CHEMBL1385640 ChEMBL CHEMBL1386751 ChEMBL CHEMBL1387694 ChEMBL CHEMBL1387840 ChEMBL CHEMBL1392406 ChEMBL CHEMBL1393068 ChEMBL CHEMBL1393076 ChEMBL CHEMBL1395082 ChEMBL CHEMBL1401415 ChEMBL CHEMBL1401616 ChEMBL CHEMBL1402584 ChEMBL CHEMBL1404682 ChEMBL CHEMBL1405684 ChEMBL CHEMBL1407638 ChEMBL CHEMBL1408394 ChEMBL CHEMBL1408519 ChEMBL CHEMBL1411315 ChEMBL CHEMBL1412379 ChEMBL CHEMBL1415358 ChEMBL CHEMBL1418989 ChEMBL CHEMBL1420755 ChEMBL CHEMBL1421533 ChEMBL CHEMBL1421893 ChEMBL CHEMBL1421945 ChEMBL CHEMBL1425139 ChEMBL CHEMBL1425961 ChEMBL CHEMBL1430509 ChEMBL CHEMBL1430619 ChEMBL CHEMBL1431093 ChEMBL CHEMBL1431321 ChEMBL CHEMBL1435182 ChEMBL CHEMBL1438166 ChEMBL CHEMBL1442527 ChEMBL CHEMBL1443767 ChEMBL CHEMBL1447650 ChEMBL CHEMBL1449698 ChEMBL CHEMBL1452205 ChEMBL CHEMBL1452358 ChEMBL CHEMBL1456482 ChEMBL CHEMBL1456840 ChEMBL CHEMBL1457455 ChEMBL CHEMBL1460821 ChEMBL CHEMBL1464894 ChEMBL CHEMBL1476435 ChEMBL CHEMBL1487890 ChEMBL CHEMBL1534570 ChEMBL CHEMBL1536441 ChEMBL L41

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: more central than 91.1% of genes in this genome.

Relative network centrality 91.1% more central than 91.1% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MTSPLPVYPVVSAHGCELSLAGGEQLVDGMSSWWAAIHGYNHPRLNAALKGQIDQMSHVMFGGITHPPAVALCRQLVAMTPASLECVFLADSGSVAVEVAMKMALQYWQAKGEPRRRFLTFRNGYHGDTFGAMSVCDPQNSMHSLWQGYLPDNLFAPAPQSRFDGEWDEMDMVPFARLMAAHRHEIAAVILEPIVQGAGGMRMYHPEWLKRVRKMCDREGILLIADEIATGFGRTGKLFACEHAGITADILCLGKALTGGTMTLSAAITTRTVAETISNGEAGCFMHGPTFMGNPLACAVASESLRLLESGEWQPQVAAIEAQLQAELAPARGSALVADVRVLGAIGVVETRRPVNMATLQRFFVEQGVWIRPFGRLIYLMPPYIITPEQLTRLTRAVNQAVQDETFFSE

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 domains and features

Domain and signature matches imported 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; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #2
0.536
Likely same site as P2Rank 1 1.5 Å 11 shared residues 92% of smaller site
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Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.312
Likely same site as FPocket 2 1.5 Å 11 shared residues 92% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.154
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.046
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.03
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Surrounding area
Site 5 P2Rank #5
0.016
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Surrounding area
All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 1

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded 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

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
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 126 records from similar proteins
Structural ligands 26 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2B1 PDB via homolog 394.3 Da · LogP 3.60 · TPSA 137.5 Open detail RCSB PDB
2B6 PDB via homolog Detail RCSB PDB
2B9 PDB via homolog Detail RCSB PDB
2BG PDB via homolog Detail RCSB PDB
3G9 PDB via homolog Detail RCSB PDB

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 RCSB PDB 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 RCSB PDB 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 RCSB PDB 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 RCSB PDB P9WQ81 164.2 Da LogP 1.75 TPSA 38.9 ✓ Ro5 ✓ Clean c1ccc2c(c1)nc(s2)CN
3G9 RCSB PDB P9WQ80 342.8 Da LogP 3.51 TPSA 40.6 ✓ Ro5 ✓ Clean CC(=O)c1ccc(cc1)N2CCN(CC2)C(=O)c3cccc(c3)Cl
3GS RCSB PDB 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 RCSB PDB P9WQ81 204.3 Da LogP 1.91 TPSA 56.0 ✓ Ro5 ✓ Clean c1ccnc(c1)c2ccc(s2)C(=O)N
3VR RCSB PDB P9WQ81 201.3 Da LogP 1.65 TPSA 29.9 ✓ Ro5 ✓ Clean CNCc1ccc(cc1)Cn2cccn2
3VS RCSB PDB P9WQ81 187.2 Da LogP 0.97 TPSA 60.9 ✓ Ro5 ✓ Clean c1cc(ccc1C(=O)N)n2ccnc2
3VW RCSB PDB P9WQ81 189.3 Da LogP 1.87 TPSA 29.1 ✓ Ro5 ✓ Clean c1ccc(cc1)C(=O)C2CCNCC2
3VX RCSB PDB P9WQ81 187.2 Da LogP 1.85 TPSA 46.2 ✓ Ro5 ✓ Clean CC(=O)Nc1ccc2c(c1)C=CC2=O
3W1 RCSB PDB P9WQ81 221.7 Da LogP 2.04 TPSA 43.8 ✓ Ro5 ✓ Clean c1cc(ccc1CN)Cn2cc(cn2)Cl
40N RCSB PDB P9WQ81 283.3 Da LogP 3.06 TPSA 51.3 ✓ Ro5 ✓ Clean c1ccc(c(c1)C2=CC(=O)c3cc4c(cc3N2)OCO4)F
41E RCSB PDB 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 RCSB PDB P9WQ81 339.4 Da LogP 3.05 TPSA 61.4 ✓ Ro5 ✓ Clean c1ccc(cc1)N2CCN(CC2)C(=O)Nc3ccc4c(c3)nns4
41N RCSB PDB P9WQ81 352.4 Da LogP 2.58 TPSA 59.1 ✓ Ro5 ✓ Clean CC(=O)c1ccc(cc1)N2CCN(CC2)C(=O)c3ccc4c(c3)OCO4
41O RCSB PDB 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 RCSB PDB P0A4X7 341.8 Da LogP 4.64 TPSA 37.4 ✓ Ro5 ✓ Clean CC(=O)c1ccc(cc1)N2CCC(CC2)C(=O)c3cccc(c3)Cl
6SR RCSB PDB P0A4X7 364.4 Da LogP 2.51 TPSA 59.1 ✓ Ro5 ✓ Clean c1cc2c(cc1C(=O)N3CCN(CC3)c4ccc5c(c4)CCC5=O)OCO2
7B9 RCSB PDB 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 RCSB PDB P12995 196.2 Da LogP 0.25 TPSA 89.3 ✓ Ro5 ✓ Clean C1=CC(C=CC1CC[C@@H](C(=O)O)N)N
FOR RCSB PDB P9WQ81 30.0 Da LogP -0.18 TPSA 17.1 ✓ Ro5 ✓ Clean C=O
J4J RCSB PDB P12995 227.2 Da LogP 0.68 TPSA 98.3 ✓ Ro5 ✓ Clean c1ccc(c(c1)[N+](=O)[O-])SCC(=O)NN
KAP RCSB PDB P9WQ81 187.2 Da LogP 0.94 TPSA 80.4 ✓ Ro5 ✓ Clean C[C@@H](C(=O)CCCCCC(=O)O)N
PL8 RCSB PDB 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 RCSB PDB 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.