Protein target profile

VK055_0552

fused predicted DNA-binding transcriptional regulator and predicted amino transferase

Genome: KpATCC43816 Gene: AIK79175.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GTI5
Length 470
Pocket druggability 0.923
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 170 total records
Functional annotation 0 EC 7 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 (%)
26.047 Lower values reduce human off-target concern.
Human E-value
5.64e-13
Gut microbiome similarity
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
28.199 Higher values support similarity to known essential genes.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
92.91 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

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 0.923
Structure A0A0H3GTI5
Pocket Pocket 1
P2Rank 0.692
Structure A0A0H3GTI5
Pocket Pocket 1
ColabFold model
FPocket 0.788 · Pocket 2
P2Rank 0.765 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 111 / 4744 genomes with a hit
Prevalence 2.3%

Cross-references

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

Chemistry

ChEMBL CHEMBL2347110 ChEMBL CHEMBL2321943 ChEMBL CHEMBL2347108 ChEMBL CHEMBL5837150 ChEMBL CHEMBL6000301 ChEMBL CHEMBL5972208 ChEMBL CHEMBL5995858 ChEMBL CHEMBL5992336 ChEMBL CHEMBL3220810 ChEMBL CHEMBL5893418 ChEMBL CHEMBL5847381 ChEMBL CHEMBL5911861 ChEMBL CHEMBL5870985 ChEMBL CHEMBL6018146 ChEMBL CHEMBL5830731 ChEMBL CHEMBL2321944 ChEMBL CHEMBL5765391 ChEMBL CHEMBL5834383 ChEMBL CHEMBL5847771 ChEMBL CHEMBL5841345 ChEMBL CHEMBL2049092 ChEMBL CHEMBL5749610 ChEMBL CHEMBL5794257 ChEMBL CHEMBL5877034 ChEMBL CHEMBL5883304 ChEMBL CHEMBL5947856 ChEMBL CHEMBL6036435 ChEMBL CHEMBL3660154 ChEMBL CHEMBL5857404 ChEMBL CHEMBL5948782 ChEMBL CHEMBL5774641 ChEMBL CHEMBL5829522 ChEMBL CHEMBL5816205 ChEMBL CHEMBL5852024 ChEMBL CHEMBL5898768 ChEMBL CHEMBL3660149 ChEMBL CHEMBL2347115 ChEMBL CHEMBL5783518 ChEMBL CHEMBL5824661 ChEMBL CHEMBL5938021 ChEMBL CHEMBL5850131 ChEMBL CHEMBL5984732 ChEMBL CHEMBL2047851 ChEMBL CHEMBL5820200 ChEMBL CHEMBL6025579 ChEMBL CHEMBL6042491 ChEMBL CHEMBL6055302 ChEMBL CHEMBL5790301 ChEMBL CHEMBL5791994 ChEMBL CHEMBL5913720 ChEMBL CHEMBL5966345 ChEMBL CHEMBL6061865 ChEMBL CHEMBL5968514 ChEMBL CHEMBL6014585 ChEMBL CHEMBL6016360 ChEMBL CHEMBL3220812 ChEMBL CHEMBL5840808 ChEMBL CHEMBL5915248 ChEMBL CHEMBL6023559 ChEMBL CHEMBL5816657 ChEMBL CHEMBL5773362 ChEMBL CHEMBL5815359 ChEMBL CHEMBL5858291 ChEMBL CHEMBL5923042 ChEMBL CHEMBL5954293 ChEMBL CHEMBL5805238 ChEMBL CHEMBL5747420 ChEMBL CHEMBL5985271 ChEMBL CHEMBL2347113 ChEMBL CHEMBL5744431 ChEMBL CHEMBL5880821 ChEMBL CHEMBL5902755 ChEMBL CHEMBL6020062 ChEMBL CHEMBL2347107 ChEMBL CHEMBL5787854 ChEMBL CHEMBL5914710 ChEMBL CHEMBL3660163 ChEMBL CHEMBL5991658 ChEMBL CHEMBL6001575 ChEMBL CHEMBL5829020 ChEMBL CHEMBL5917834 ChEMBL CHEMBL5943643 ChEMBL CHEMBL5748738 ChEMBL CHEMBL5938703 ChEMBL CHEMBL3660157 ChEMBL CHEMBL6065206 ChEMBL CHEMBL2047861 ChEMBL CHEMBL2049095 ChEMBL CHEMBL5743448 ChEMBL CHEMBL5915177 ChEMBL CHEMBL6001864 ChEMBL CHEMBL6051643 ChEMBL CHEMBL2049094 ChEMBL CHEMBL5785687 ChEMBL CHEMBL5874999 ChEMBL CHEMBL2347112 ChEMBL CHEMBL3660169 ChEMBL CHEMBL5772534 ChEMBL CHEMBL6036370 ChEMBL CHEMBL6054133

Metabolic context

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

Explore metabolic network

Metabolic context: more central than 99.1% of genes in this genome.

Relative network centrality 99.1% more central than 99.1% 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.

MKKYQQLAQQLTEQIALGVWLPGDRLPSLREQVISSGMSFMTVSHAYQLLESQGRIVARPQSGYYVAPQPVKLRQPAPPAQVTRDEAVDINTYIFEVLQASRQASMLPFASAFPDPRLFPLQQLNRSLAQVSKTATAMSVIENLPPGNAELRHAIARRYALQGMNVSPDEIVITAGALEALNLSLQAVTEPGDWVVVENPCFYGALQALERLRLKALSVATDVREGIDLTALEAALQNYPVKACWLMTNGQNPLGFTLSAEKKAALVALLARYNVMLIEDDVYSELYFGREKPLPAKFWDRQEMTLHCSSFSKCLVPGFRIGWVAAGKQARRIQQLQLMSTLSTSSPMQLALVDYLSTKRYDAHLRRLRRQLAERKQQAWQALLRHLPPEVIVHHSDSGYFLWIELPEGADASALSARALASHISIAPGKMFSTSDSWTSFFRFNTAWGWGEREEQGVKRLGELIREQLA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Gene Ontology (GO)

7
  • 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:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
  • 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.
  • 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0008483 Catalysis of the transfer of an amino group to an acceptor, usually a 2-oxo acid.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records
Show feature table
Start End DB Term Name
100 465 Gene3D G3DSA:3.90.1150.10 Aspartate Aminotransferase, domain 1
100 465 InterPro IPR015422 Pyridoxal phosphate-dependent transferase, small domain
1 67 Gene3D G3DSA:1.10.10.10 -
1 67 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
141 360 FunFam G3DSA:3.40.640.10:FF:000023 Transcriptional regulator, GntR family
3 66 Pfam PF00392 Bacterial regulatory proteins, gntR family
3 66 InterPro IPR000524 Transcription regulator HTH, GntR
2 93 FunFam G3DSA:1.10.10.10:FF:000320 GntR family transcriptional regulator
2 67 CDD cd07377 WHTH_GntR
2 67 InterPro IPR000524 Transcription regulator HTH, GntR
141 360 Gene3D G3DSA:3.40.640.10 -
141 360 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
94 469 PANTHER PTHR42790 AMINOTRANSFERASE
146 447 Pfam PF00155 Aminotransferase class I and II
146 447 InterPro IPR004839 Aminotransferase, class I/classII
107 463 CDD cd00609 AAT_like
2 70 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
2 70 InterPro IPR036390 Winged helix DNA-binding domain superfamily
7 66 SMART SM00345 gntr3
7 66 InterPro IPR000524 Transcription regulator HTH, GntR
92 467 SUPERFAMILY SSF53383 PLP-dependent transferases
92 467 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
1 69 ProSiteProfiles PS50949 GntR-type HTH domain profile.
1 69 InterPro IPR000524 Transcription regulator HTH, GntR

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 #1
0.923
Likely same site as P2Rank 1 1.8 Å 14 shared residues 93% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.692
Likely same site as FPocket 1 1.8 Å 14 shared residues 93% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.397
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.072
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.028
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.012
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

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
AlphaFold DB AF_A0A0H3GTI5
AlphaFold DB full sequence Viewing
ColabFold VK055_0552
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.

170 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 120 records from similar proteins
Structural ligands 20 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
09M PDB via homolog 407.3 Da · LogP 1.87 · TPSA 154.1 Open detail RCSB PDB
0K5 PDB via homolog Detail RCSB PDB
0KE PDB via homolog Detail RCSB PDB
0L0 PDB via homolog Detail RCSB PDB
0LD 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
09M RCSB PDB Q8N5Z0 407.3 Da LogP 1.87 TPSA 154.1 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=Cc3ccccc3N(C2=O)O…
0K5 RCSB PDB Q8N5Z0 499.4 Da LogP 3.66 TPSA 163.4 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=Cc3cc(ccc3N(C2=O)…
0KE RCSB PDB Q8N5Z0 437.3 Da LogP 1.88 TPSA 163.4 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=Cc3ccc(cc3N(C2=O)…
0L0 RCSB PDB Q8N5Z0 527.5 Da LogP 3.47 TPSA 163.4 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=Cc3cc(c(cc3N(C2=O…
0LD RCSB PDB Q8N5Z0 473.4 Da LogP 2.05 TPSA 172.0 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=Cc3cn(nc3N(C2=O)O…
0X1 RCSB PDB Q8N5Z0 523.4 Da LogP 3.60 TPSA 171.3 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CNC2=Cc3cc(ccc3N4C2=NN…
3EE RCSB PDB O57946 207.2 Da LogP 0.50 TPSA 97.5 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)CC(=O)C(=O)O)N
7AR RCSB PDB Q8N5Z0 364.2 Da LogP 3.29 TPSA 74.7 ✓ Ro5 ✓ Clean c1ccc(cc1)C[C@H](C(=O)O)N2C(=O)c3cc(c(cc3C2=O)C…
AKG RCSB PDB O57946 146.1 Da LogP -0.50 TPSA 91.7 ✓ Ro5 ✓ Clean C(CC(=O)O)C(=O)C(=O)O
BF5 RCSB PDB Q8N5Z0 363.4 Da LogP -0.55 TPSA 105.3 ✓ Ro5 ✓ Clean C[C@H]1COC2=C3N1C=C(C(=C3CC(=C2N4CCN(CC4)N)F)O)…
G9A RCSB PDB O57946 130.1 Da LogP 0.10 TPSA 74.6 ✓ Ro5 ✓ Clean C(/C=C/C(=O)O)C(=O)O
HCI RCSB PDB Q75WK2 150.2 Da LogP 1.70 TPSA 37.3 ✓ Ro5 ✓ Clean c1ccc(cc1)CCC(=O)O
KMT RCSB PDB Q75WK2 148.2 Da LogP 0.39 TPSA 54.4 ✓ Ro5 ✓ Clean CSCCC(=O)C(=O)O
KYA RCSB PDB O57946 189.2 Da LogP 1.64 TPSA 70.4 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(cc(n2)C(=O)O)O
KYN RCSB PDB Q8N5Z0 208.2 Da LogP 0.25 TPSA 106.4 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)C[C@@H](C(=O)O)N)N
MVQ RCSB PDB Q8N5Z0 453.6 Da LogP 2.57 TPSA 89.4 ✓ Ro5 ✓ Clean CN1C(=O)c2c(sc(n2)N3CCC[C@@H]3C(=O)NCc4ccccc4)N…
MVT RCSB PDB Q8N5Z0 441.5 Da LogP 4.74 TPSA 72.0 ✓ Ro5 ✓ Clean CC(C)[C@@H](Cc1nnc(s1)NS(=O)(=O)c2cc(cc(c2)F)F)…
N5F RCSB PDB Q72LL6 392.3 Da LogP 0.50 TPSA 186.5 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCCC(=O)O)C(=…
PGU RCSB PDB Q72LL6 378.3 Da LogP 0.11 TPSA 186.5 1 viol. ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCC(=O)O)C(=O…
PMP RCSB PDB O57946 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.