Protein target profile

KP13_00978

Menaquinone-specific isochorismate synthase

Genome: KpKP13 Gene: menF AHE43492.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GT11
Length 429
Pocket druggability 0.887
Direct ligand evidence 0 70 total records
Functional annotation 1 EC 4 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
No hit
Gut microbiome similarity
1.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
95.92 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 0.887
Structure A0A0H3GT11
Pocket Pocket 1
P2Rank 0.888
Structure A0A0H3GT11
Pocket Pocket 1
ColabFold model
FPocket 0.37 · Pocket 1
P2Rank 0.897 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 63 / 4744 genomes with a hit
Prevalence 1.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MLSVSTALARLQDGLGESFPDSPGTRIIDVAFLLNDAFDPLLWCGQQAQWPQFYWQQRNGDEELATLGAVKTFTSLDAANRFLRQAGRQDLRICGLNAFEPQQGSLALPRLEWRRCGGRAVLRLVLHSDISLREDAATARAFLASLTTTQATPGAIPPLLSERHSSDYPQWQAMIARATKAISAGEMDKVVLARATDLQFAAPLDAVSIMAASRRSNLNCFHFLMAFNARQAFFGSTPERLWRRRGALLRTEALAGTVANHQEDAKAQQLADWLMKDDKNQRENMLVVEDICQRLQSEASTLDVLPPQVVRLRKVQHLRRCIWTELAAPDDSRCLLQLQPTAAVAGLPRRAALAFIQRHEPFSREWYAGSAGYLSLAQSEFCVALRSAKVDHDTLRLYAGAGIVSGSDAQQEWQEIDNKAAGLRSLLCP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0009234 The chemical reactions and pathways resulting in the formation of any of the menaquinones. Structurally, menaquinones consist of a methylated naphthoquinone ring structure and side chains composed of a variable number of unsaturated isoprenoid residues. Menaquinones that have vitamin K activity and are known as vitamin K2.
  • 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:0008909 Catalysis of the reaction: chorismate = isochorismate.
  • GO:0000287 Binding to a magnesium (Mg) ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
3 429 Hamap MF_01935 Isochorismate synthase MenF [menF].
3 429 InterPro IPR034681 Isochorismate synthase MenF
92 426 NCBIfam TIGR00543 isochorismate synthase
92 426 InterPro IPR004561 Isochorismate synthase
9 427 PANTHER PTHR47253 -
9 427 InterPro IPR044250 Isochorismate synthase MenF-like
1 428 Gene3D G3DSA:3.60.120.10 Anthranilate synthase
1 428 InterPro IPR005801 ADC synthase
24 427 SUPERFAMILY SSF56322 ADC synthase
24 427 InterPro IPR005801 ADC synthase
1 429 FunFam G3DSA:3.60.120.10:FF:000002 Isochorismate synthase MenF
169 419 Pfam PF00425 chorismate binding enzyme
169 419 InterPro IPR015890 Chorismate-utilising enzyme, C-terminal

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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.887
Likely same site as P2Rank 1 0.9 Å 23 shared residues 96% of smaller site
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #19
0.264
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.888
Likely same site as FPocket 1 0.9 Å 23 shared residues 96% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.105
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.1
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.046
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.046
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:189-189 Proton acceptor
UniProt: Active site:239-239 Proton donor
UniProt: Binding site:283-283
UniProt: Binding site:415-415
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_A0A0H3GT11
AlphaFold DB full sequence Viewing
ColabFold KP13_00978
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.

70 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 20 records from similar proteins
Structural ligands 6 0 loaded crystals
Measured bioactivity 14 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
15P PDB via homolog 1529.8 Da · LogP 0.17 · TPSA 334.1 Open detail RCSB PDB
ISC PDB via homolog Detail RCSB PDB
ISJ PDB via homolog Detail RCSB PDB
PYR PDB via homolog Detail RCSB PDB
SAL 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
15P RCSB PDB A0A6H3A7J7 1529.8 Da LogP 0.17 TPSA 334.1 2 viol. ✓ Clean COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO…
ISC RCSB PDB P0AEJ3 226.2 Da LogP -0.09 TPSA 104.1 ✓ Ro5 ✓ Clean C=C(C(=O)O)O[C@H]1C=CC=C([C@@H]1O)C(=O)O
ISJ RCSB PDB P0AEJ3 226.2 Da LogP -0.09 TPSA 104.1 ✓ Ro5 ✓ Clean C=C(C(=O)O)O[C@@H]1C=C(C=C[C@H]1O)C(=O)O
PYR RCSB PDB Q9X9I8 88.1 Da LogP -0.34 TPSA 54.4 ✓ Ro5 ✓ Clean CC(=O)C(=O)O
SAL RCSB PDB Q9X9I8 138.1 Da LogP 1.09 TPSA 57.5 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)O)O
TAR RCSB PDB P38051 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.