KpATCC43816 Protein target profile

bacterial regulatory, gntR family protein

Accession: VK055_2111

Gene: AIK80717.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GJ88
Length 483
Pocket druggability (P2Rank · AlphaFold DB model) 0.855
Direct ligand evidence 0 171 total records
Functional annotation 0 EC 6 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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 (%)
24.37 Lower values reduce human off-target concern.
Human E-value
9e-09
Gut microbiome similarity
0.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
92.83 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.855
Structure A0A0H3GJ88
Pocket Pocket 1
Druggability (FPocket) 0.867
Structure A0A0H3GJ88
Pocket Pocket 24
ColabFold model
P2Rank 0.754 · Pocket 1
FPocket 0.651 · Pocket 4
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 30 / 4744 genomes with a hit
Prevalence 0.6%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MNIPDEGFFTLLTQGMRNRTVETLQRALYHTLRDAILQGTLTARCRLPGSRVMAERLHLSRNTVNAALEQLALEGYLTRSRQGTQVAPLASCRQEAGQMPPVVLPERLQWLPAAMRRDSPTLAFTPGMPAVNYFPLPLWRRLMDNVLREDGSALLGYGEAAGDPLLREAIARHLALSRGIRCDIRQIVITEGALEGVNLCASLLTNPGDSVWLEEPGYLGARSGFQRAGLRVRGMAVDDEGMCIANGVAEPPRLIFTSPSHQYPCGSIMSAGRRLALVEYARRHGAWIVEDDYDSEFRHSGEPIPAMLGMVPDAPVVYLGTFSKTLFPALRIGFMVMPPALADAAQDAIGALLRGGHRAEQRALASFIEKGHYARHLAAMRRLYRKRQQQLREALAQEITVPCDVLGGGGGMHLTVAMEGVNDRTLAQQARQFQLAPAALSHFYLDPQRARSGLVLGYGNTSASRYLPALWTLNRLIAQHRRA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
Cytoplasmic

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: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).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
28 86 SMART SM00345 gntr3
28 86 InterPro IPR000524 Transcription regulator HTH, GntR
103 480 SUPERFAMILY SSF53383 PLP-dependent transferases
103 480 InterPro IPR015424 Pyridoxal phosphate-dependent transferase
13 97 Gene3D G3DSA:1.10.10.10 -
13 97 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
47 61 PRINTS PR00035 GntR bacterial regulatory protein HTH signature
47 61 InterPro IPR000524 Transcription regulator HTH, GntR
61 77 PRINTS PR00035 GntR bacterial regulatory protein HTH signature
61 77 InterPro IPR000524 Transcription regulator HTH, GntR
25 83 Pfam PF00392 Bacterial regulatory proteins, gntR family
25 83 InterPro IPR000524 Transcription regulator HTH, GntR
111 469 Gene3D G3DSA:3.40.640.10 -
111 469 InterPro IPR015421 Pyridoxal phosphate-dependent transferase, major domain
147 429 Pfam PF00155 Aminotransferase class I and II
147 429 InterPro IPR004839 Aminotransferase, class I/classII
23 90 SUPERFAMILY SSF46785 Winged helix DNA-binding domain
23 90 InterPro IPR036390 Winged helix DNA-binding domain superfamily
377 397 Coils Coil Coil
124 430 CDD cd00609 AAT_like
19 477 PANTHER PTHR46577 HTH-TYPE TRANSCRIPTIONAL REGULATORY PROTEIN GABR
22 89 ProSiteProfiles PS50949 GntR-type HTH domain profile.
22 89 InterPro IPR000524 Transcription regulator HTH, GntR
23 87 CDD cd07377 WHTH_GntR
23 87 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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.855
Likely same site as FPocket 24 4.7 Å 17 shared residues 77% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.074
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.065
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.034
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.032
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #24
0.867 Unusual size
Likely same site as P2Rank 1 4.7 Å 17 shared residues 77% of smaller site
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_A0A0H3GJ88
AlphaFold DB full sequence Viewing
ColabFold VK055_2111
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.

171 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 121 records from similar proteins
Structural ligands 21 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
76U RCSB PDB P94426 366.3 Da LogP 1.00 TPSA 149.2 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN[C@@H](CCC(=O)O)CF)O
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…
ABU RCSB PDB P94426 103.1 Da LogP -0.19 TPSA 63.3 ✓ Ro5 ✓ Clean C(CC(=O)O)CN
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
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 Q8N5Z0 248.2 Da LogP 0.16 TPSA 125.9 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)CN)O
QL4 RCSB PDB P94426 438.4 Da LogP 2.44 TPSA 158.8 ✓ Ro5 ✓ Clean Cc1c(c(c(cn1)COP(=O)(O)O)/C=N/[C@@H](CCC(=O)O)C…

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.

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