Protein target profile

KP13_05447

Psp operon transcriptional activator

Genome: KpKP13 Gene: AHE44963.1 pspF 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GS68
Length 329
Pocket druggability 0.147
Direct ligand evidence 0 56 total records
Functional annotation 0 EC 5 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
No hit
Gut microbiome similarity
2.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
40.684 Higher values support similarity to known essential genes.
DEG E-value
3.82e-62 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
86.84 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 0.147
Structure A0A0H3GS68
Pocket Pocket 2
P2Rank 0.455
Structure A0A0H3GS68
Pocket Pocket 1
ColabFold model
FPocket 0.464 · Pocket 1
P2Rank 0.356 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 129 / 4744 genomes with a hit
Prevalence 2.7%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MAKFIMAQYKDNLLGEANSFLEVLEQVSRLAPLDKPVLVIGERGTGKELIANRLHYLSSRWQGPFISLNCAALNDNLLDSELFGHEAGAFTGASKRHPGRFERADGGTLFLDELATAPMLVQEKLLRVIEYGELERVGGSQPLQVNVRLVCATNADLPQMVEEGHFRADLLDRLAFDVVQLPPLRDRQSDIMLLANQFAIQMCRELGLPLFPGFSERATATLLGYRWPGNIRELKNVVERSVYRHGDSEHELDAIIINPFRQSPGSPPEAAPGDELPALPLDLRDFQLQQEKRLLQRSLEQAKYHQKQAAELLGLTYHQLRALLKKHQL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
  • GO:0008134 Binding to a transcription factor, a protein required to initiate or regulate transcription.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
6 183 FunFam G3DSA:3.40.50.300:FF:000006 DNA-binding transcriptional regulator NtrC
13 327 NCBIfam TIGR02974 phage shock protein operon transcriptional activator
13 327 InterPro IPR014317 Transcription activator PspF
12 328 PANTHER PTHR32071 TRANSCRIPTIONAL REGULATORY PROTEIN
273 329 Gene3D G3DSA:1.10.10.60 -
33 185 SMART SM00382 AAA_5
33 185 InterPro IPR003593 AAA+ ATPase domain
14 175 Pfam PF00158 Sigma-54 interaction domain
14 175 InterPro IPR002078 RNA polymerase sigma factor 54 interaction domain
99 114 ProSitePatterns PS00676 Sigma-54 interaction domain ATP-binding region B signature.
99 114 InterPro IPR025943 Sigma-54 interaction domain, ATP-binding site 2
293 310 PRINTS PR01590 FIS bacterial regulatory protein HTH signature
293 310 InterPro IPR002197 DNA binding HTH domain, Fis-type
310 329 PRINTS PR01590 FIS bacterial regulatory protein HTH signature
310 329 InterPro IPR002197 DNA binding HTH domain, Fis-type
13 243 ProSiteProfiles PS50045 Sigma-54 interaction domain profile.
13 243 InterPro IPR002078 RNA polymerase sigma factor 54 interaction domain
22 183 CDD cd00009 AAA
185 266 Gene3D G3DSA:1.10.8.60 -
3 184 Gene3D G3DSA:3.40.50.300 -
3 184 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
290 326 Pfam PF02954 Bacterial regulatory protein, Fis family
290 326 InterPro IPR002197 DNA binding HTH domain, Fis-type
14 253 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
14 253 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
227 329 SUPERFAMILY SSF46689 Homeodomain-like
227 329 InterPro IPR009057 Homeobox-like domain superfamily
227 236 ProSitePatterns PS00688 Sigma-54 interaction domain C-terminal part signature.
227 236 InterPro IPR025944 Sigma-54 interaction domain, conserved site

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

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

Site 1 P2Rank #1
0.455
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.015
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.008
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.008
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_A0A0H3GS68
AlphaFold DB full sequence Viewing
ColabFold KP13_05447
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.

56 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 6 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
08T PDB via homolog Open detail RCSB PDB
5QT PDB via homolog Detail RCSB PDB
AGS PDB via homolog Detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
AZU 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
08T RCSB PDB O67198 [Be](OP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@…
5QT RCSB PDB Q1ZS18 272.3 Da LogP 0.83 TPSA 99.9 ✓ Ro5 ✓ Clean CC(C)(C)COC(=O)CNC1=NNC(=O)NC1=S
AGS RCSB PDB G3XCV0 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB A0A0H3AHP1 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AZU RCSB PDB Q1ZS18 273.3 Da LogP 0.14 TPSA 104.9 ✓ Ro5 ✓ Clean CC(C)(C)COC(=O)CSC1=NNC(=O)NC1=O
C2E RCSB PDB G3XCV0 690.4 Da LogP -3.05 TPSA 349.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=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.