Protein target profile

KP13_00581

6-phosphofructokinase

Genome: KpKP13 Gene: pfkA AHE47056.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GGY4
Length 320
Pocket druggability 0.066
Direct ligand evidence 0 59 total records
Functional annotation 1 EC 13 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 (%)
57.778 Lower values reduce human off-target concern.
Human E-value
6.1e-09
Gut microbiome similarity
21.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
72.188 Higher values support similarity to known essential genes.
DEG E-value
8.46e-173 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.17 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 0.066
Structure A0A0H3GGY4
Pocket Pocket 7
P2Rank 0.544
Structure A0A0H3GGY4
Pocket Pocket 1
ColabFold model
FPocket 0.547 · Pocket 6
P2Rank 0.652 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1016 / 4744 genomes with a hit
Prevalence 21.4%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MIKKIGVLTSGGDAPGMNAAIRGVVRAALTEGLEVFGIYDGYLGLYEDRMVQLDRYSVSDMINRGGTFLGSARFPEFREEHIRAVAIENMKKRGLDALVVIGGDGSYMGAMRLTEMGFPCIGLPGTIDNDIKGTDYTIGFFTALSTVVEAIDRLRDTSSSHQRISVVEVMGRYCGDLTLAAAIAGGCEFIMVPEVEYTRDDLVAEIKAGIAKGKKHAIVAITEHMCDVDELASYIEKETGRETRATVLGHIQRGGSPVPYDRILASRMGAYAIELLLQGHGGRCVGIQNEKLVHHDIIDAIENMKRPFKNDWLDCAKKLY

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 13 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

13
  • GO:0008443 Catalysis of the transfer of a phosphate group, usually from ATP, to a phosphofructose substrate molecule.
  • GO:0006002 The chemical reactions and pathways involving fructose 6-phosphate, also known as F6P. The D-enantiomer is an important intermediate in glycolysis, gluconeogenesis, and fructose metabolism.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003872 Catalysis of the reaction: ATP + D-fructose-6-phosphate = ADP + D-fructose 1,6-bisphosphate.
  • GO:0006096 The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
  • GO:0005945 A protein complex that possesses 6-phosphofructokinase activity; homodimeric, homooctameric, and allosteric homotetrameric forms are known.
  • GO:0016208 Binding to AMP, adenosine monophosphate.
  • GO:0070095 Binding to fructose 6-phosphate.
  • GO:0042802 Binding to an identical protein or proteins.
  • GO:0046872 Binding to a metal ion.
  • GO:0048029 Binding to a monosaccharide. Monosaccharides are the simplest carbohydrates; they are polyhydroxy aldehydes H[CH(OH)]nC(=O)H or polyhydroxy ketones H[CHOH]nC(=O)[CHOH]mH with three or more carbon atoms. They form the constitutional repeating units of oligo- and polysaccharides.
  • GO:0061621 The glycolytic process that begins with the conversion of glucose to glucose-6-phosphate by glucokinase activity. Glycolytic processes are the chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP.
  • GO:0030388 The chemical reactions and pathways involving fructose 1,6-bisphosphate, also known as FBP. The D enantiomer is a metabolic intermediate in glycolysis and gluconeogenesis.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

38 records
Show feature table
Start End DB Term Name
3 320 CDD cd00763 Bacterial_PFK
3 320 InterPro IPR012828 ATP-dependent 6-phosphofructokinase, prokaryotic
3 311 SUPERFAMILY SSF53784 Phosphofructokinase
3 311 InterPro IPR035966 Phosphofructokinase superfamily
244 262 ProSitePatterns PS00433 Phosphofructokinase signature.
244 262 InterPro IPR015912 Phosphofructokinase, conserved site
4 276 Pfam PF00365 Phosphofructokinase
4 276 InterPro IPR000023 Phosphofructokinase domain
2 320 Hamap MF_00339 ATP-dependent 6-phosphofructokinase [pfkA].
2 320 InterPro IPR012828 ATP-dependent 6-phosphofructokinase, prokaryotic
4 301 NCBIfam TIGR02482 6-phosphofructokinase
4 301 InterPro IPR012828 ATP-dependent 6-phosphofructokinase, prokaryotic
3 305 PANTHER PTHR13697 PHOSPHOFRUCTOKINASE
143 252 Gene3D G3DSA:3.40.50.460 Phosphofructokinase domain
143 252 InterPro IPR035966 Phosphofructokinase superfamily
4 168 FunFam G3DSA:3.40.50.450:FF:000001 ATP-dependent 6-phosphofructokinase
4 280 Gene3D G3DSA:3.40.50.450 -
1 320 PIRSF PIRSF000532 ATP_PFK_prok
1 320 InterPro IPR012003 ATP-dependent 6-phosphofructokinase, prokaryotic-type
7 26 PRINTS PR00476 ATP-dependent phosphofructokinase family signature
7 26 InterPro IPR022953 ATP-dependent 6-phosphofructokinase
32 45 PRINTS PR00476 ATP-dependent phosphofructokinase family signature
32 45 InterPro IPR022953 ATP-dependent 6-phosphofructokinase
139 157 PRINTS PR00476 ATP-dependent phosphofructokinase family signature
139 157 InterPro IPR022953 ATP-dependent 6-phosphofructokinase
213 225 PRINTS PR00476 ATP-dependent phosphofructokinase family signature
213 225 InterPro IPR022953 ATP-dependent 6-phosphofructokinase
177 194 PRINTS PR00476 ATP-dependent phosphofructokinase family signature
177 194 InterPro IPR022953 ATP-dependent 6-phosphofructokinase
240 262 PRINTS PR00476 ATP-dependent phosphofructokinase family signature
240 262 InterPro IPR022953 ATP-dependent 6-phosphofructokinase
159 175 PRINTS PR00476 ATP-dependent phosphofructokinase family signature
159 175 InterPro IPR022953 ATP-dependent 6-phosphofructokinase
94 110 PRINTS PR00476 ATP-dependent phosphofructokinase family signature
94 110 InterPro IPR022953 ATP-dependent 6-phosphofructokinase
121 138 PRINTS PR00476 ATP-dependent phosphofructokinase family signature
121 138 InterPro IPR022953 ATP-dependent 6-phosphofructokinase
143 252 FunFam G3DSA:3.40.50.460:FF:000002 ATP-dependent 6-phosphofructokinase

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
0.544
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.034
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:128-128 Proton acceptor
UniProt: Binding site:103-106
UniProt: Binding site:104-104
UniProt: Binding site:12-12
UniProt: Binding site:126-128 in other chain
UniProt: Binding site:155-155 in other chain
UniProt: Binding site:163-163
UniProt: Binding site:170-172 in other chain
UniProt: Binding site:186-188 in other chain
UniProt: Binding site:212-212 in other chain
UniProt: Binding site:214-216 in other chain
UniProt: Binding site:22-26
UniProt: Binding site:223-223 in other chain
UniProt: Binding site:244-244
UniProt: Binding site:250-253 in other chain
UniProt: Binding site:55-60
UniProt: Binding site:73-74
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_A0A0H3GGY4
AlphaFold DB full sequence Viewing
ColabFold KP13_00581
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.

59 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 9 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 3 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
ACP PDB via homolog 505.2 Da · LogP -1.52 · TPSA 269.9 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
F6P PDB via homolog Detail RCSB PDB
FLC PDB via homolog Detail RCSB PDB
PEP 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
ACP RCSB PDB Q01813 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP RCSB PDB Q2FXM8 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)…
F6P RCSB PDB P99165 260.1 Da LogP -3.10 TPSA 156.9 1 viol. ✓ Clean C([C@@H]1[C@H]([C@@H]([C@](O1)(CO)O)O)O)OP(=O)(…
FLC RCSB PDB P99165 189.1 Da LogP -5.25 TPSA 140.6 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O
PEP RCSB PDB P00512 168.0 Da LogP -0.31 TPSA 104.1 ✓ Ro5 ✓ Clean C=C(C(=O)O)OP(=O)(O)O
PGA RCSB PDB P00512 156.0 Da LogP -0.82 TPSA 104.1 ✓ Ro5 ✓ Clean C(C(=O)O)OP(=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.