KpKP13 Protein target profile

Isochorismatase

Accession: KP13_03397

Gene: entB AHE45775.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GPR5
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Length 283
Pocket druggability (P2Rank · AlphaFold DB model) 0.668
Direct ligand evidence 0 58 total records
Functional annotation 2 EC 5 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

Independent pocket support: P2Rank + FPocket Both predictors report a high-scoring binding site (P2Rank 0.67, FPocket 0.78). Use the 3D pocket comparison to verify whether they identify the same site. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.78. This is a computational pocket signal, not binding validation. Review the complete evidence below

Risks to review

Microbiome similarity 99 of 4744 screened genomes (2.1%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.67) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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
2.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
48.464 Higher values support similarity to known essential genes.
DEG E-value
4.15e-96 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.46 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) 0.668
Structure A0A0H3GPR5
Pocket Pocket 1
Druggability (FPocket) 0.775
Structure A0A0H3GPR5
Pocket Pocket 1
ColabFold model
P2Rank 0.697 · Pocket 1
FPocket 0.768 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 99 / 4744 genomes with a hit
Prevalence 2.1%

Sequence

Primary amino-acid sequence viewer.

MAIPKLQAYALPEASDIPANKVNWAFEPSRAALLIHDMQEYFLNFWGENSAMMEKVVANIAALRDFCKQNGIPVYYTAQPKEQSDEDRALLNDMWGPGLTRSPEQQQVIAALAPDEDDTVLVKWRYSAFHRSPLEEMLKETGRDQLIITGVYAHIGCMTTATDAFMRDIKPFFVADALADFSREEHLMALKYVAGRSGRVVMTEELLPLPASKAALRELILPLLDESDEPLDDENLIDYGLDSVRMMALAARWRKVHGDIDFVMLAKNPTIDAWWALLSREVH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

2

Gene Ontology (GO)

5
  • GO:0008908 Catalysis of the reaction: H2O + isochorismate = 2,3-dihydroxy-2,3-dihydrobenzoate + pyruvate.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0047527 Catalysis of the reaction: ATP + 2,3-dihydroxybenzoate + L-serine = products of ATP breakdown + N-(2,3-dihydroxybenzoyl)-L-serine.
  • GO:0046872 Binding to a metal ion.
  • GO:0009239 The chemical reactions and pathways resulting in the formation of enterobactin, a catechol-derived siderochrome of Enterobacteria; enterobactin (N',N',N''-(2,6,10-trioxo-1,5,9-triacyclodecane-3,7,11-triyl)tris(2,3-dihydroxy)benzamide) is a self-triester of 2,3-dihydroxy-N-benzoyl-L-serine and a product of the shikimate pathway.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

31 records
Show feature table
Start End DB Term Name
1 283 PIRSF PIRSF001111 Isochorismatase
1 283 InterPro IPR016291 Isochorismatase
2 14 PRINTS PR01398 Isochorismatase signature
2 14 InterPro IPR016291 Isochorismatase
80 99 PRINTS PR01398 Isochorismatase signature
80 99 InterPro IPR016291 Isochorismatase
186 203 PRINTS PR01398 Isochorismatase signature
186 203 InterPro IPR016291 Isochorismatase
112 134 PRINTS PR01398 Isochorismatase signature
112 134 InterPro IPR016291 Isochorismatase
63 80 PRINTS PR01398 Isochorismatase signature
63 80 InterPro IPR016291 Isochorismatase
168 186 PRINTS PR01398 Isochorismatase signature
168 186 InterPro IPR016291 Isochorismatase
215 274 Pfam PF00550 Phosphopantetheine attachment site
215 274 InterPro IPR009081 Phosphopantetheine binding ACP domain
1 207 FunFam G3DSA:3.40.50.850:FF:000002 Vibriobactin-specific isochorismatase
211 278 SUPERFAMILY SSF47336 ACP-like
211 278 InterPro IPR036736 ACP-like superfamily
23 207 PANTHER PTHR43540 PEROXYUREIDOACRYLATE/UREIDOACRYLATE AMIDOHYDROLASE-RELATED
2 204 CDD cd01013 isochorismatase
32 205 Pfam PF00857 Isochorismatase family
32 205 InterPro IPR000868 Isochorismatase-like
208 283 FunFam G3DSA:1.10.1200.10:FF:000009 Isochorismatase
211 283 Gene3D G3DSA:1.10.1200.10 -
211 283 InterPro IPR036736 ACP-like superfamily
207 282 ProSiteProfiles PS50075 Carrier protein (CP) domain profile.
207 282 InterPro IPR009081 Phosphopantetheine binding ACP domain
1 210 Gene3D G3DSA:3.40.50.850 -
1 210 InterPro IPR036380 Isochorismatase-like superfamily
1 210 SUPERFAMILY SSF52499 Isochorismatase-like hydrolases

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
0.668
Likely same site as FPocket 1 1.8 Å 14 shared residues 78% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.009
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.775
Likely same site as P2Rank 1 1.8 Å 14 shared residues 78% of smaller site
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Surrounding area
Pocket 2 FPocket #2
0.264
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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_A0A0H3GPR5
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_03397
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.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1HZ PDB via homolog 466.5 Da · LogP -1.40 · TPSA 205.9 Open detail RCSB PDB
BTB PDB via homolog Detail RCSB PDB
C5J PDB via homolog Detail RCSB PDB
ISC PDB via homolog Detail RCSB PDB
NH4 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
1HZ RCSB PDB
4IZ6
P0ADI4 466.5 Da LogP -1.40 TPSA 205.9 2 viol. Alert c1cc(c(c(c1)O)O)CCS(=O)(=O)NC[C@@H]2[C@H]([C@H]…
BTB RCSB PDB
5BK6
Q1M7F4 209.2 Da LogP -3.01 TPSA 104.4 ✓ Ro5 ✓ Clean C(CO)N(CCO)C(CO)(CO)CO
C5J RCSB PDB
6AZQ
Q1M7F4 103.1 Da LogP -1.27 TPSA 98.2 ✓ Ro5 ✓ Clean C(=O)(N)NC(=O)N
ISC RCSB PDB
3TG2
P0C6D3 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
NH4 RCSB PDB
3HB7
A6TWT6 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
PNS RCSB PDB
3RG2
P0ADI4 358.4 Da LogP -0.96 TPSA 145.2 1 viol. ✓ Clean CC(C)(COP(=O)(O)O)[C@H](C(=O)NCCC(=O)NCCS)O
QLI RCSB PDB
3R77
Q51790 225.2 Da LogP -0.12 TPSA 109.9 ✓ Ro5 ✓ Clean C=C(C(=O)O)O[C@H]1C=CC=C([C@@H]1N)C(=O)O
SVS RCSB PDB
3RG2
P0ADI4 450.5 Da LogP -1.10 TPSA 185.7 1 viol. ✓ Clean c1ccc(c(c1)CCS(=O)(=O)NC[C@@H]2[C@H]([C@H]([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.

Sequence

UniProt A0A0H3GPR5