Protein target profile

KP13_02140

Outer membrane pore protein E

Genome: KpKP13 Gene: phoE AHE46146.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GIV3
Length 350
Pocket druggability 0.996
Direct ligand evidence 0 65 total records
Functional annotation 0 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.

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
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
84.615 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization
OuterMembrane

Structure confidence

ColabFold pLDDT
93.14 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 0.996
Structure A0A0H3GIV3
Pocket Pocket 3
P2Rank 0.679
Structure A0A0H3GIV3
Pocket Pocket 1
ColabFold model
FPocket 0.667 · Pocket 18
P2Rank 0.538 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 110 / 4744 genomes with a hit
Prevalence 2.3%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKKSTLALMMMGFVASTATQAAEVYNKNANKLDVYGKIKAMHYFSDYDSKDGDQTYVRFGIKGETQINDDLTGYGRWESEFSGNKTESDSSQKTRLAFAGVKLKNYGSFDYGRNLGALYDVEAWTDMFPEFGGDSSAQTDNFMTKRASGLATYRNTDFFGLVDGLDLTLQYQGKNEGREAKKQNGDGVGTSLSYDFGGSDFAVSAAYTSSDRTNDQNLLARGQGSKAEAWATGLKYDANNIYLATMYSETRKMTPISGGFANKAQNFEAVAQYQFDFGLRPSLGYVLSKGKDIEGVGSEDLVNYIDVGLTYYFNKNMNAFVDYKINQLKSDNKLGINDDDIVALGMTYQF

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0034220 A process in which a monoatomic ion is transported across a membrane. Monatomic ions (also called simple ions) are ions consisting of exactly one atom.
  • GO:0015288 Enables the transfer of substances, sized less than 1000 Da, from one side of a membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
  • GO:0046930 A protein complex providing a discrete opening in a membrane that allows the passage of gases and/or liquids.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

40 records
Show feature table
Start End DB Term Name
22 350 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
5 16 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
94 104 PRINTS PR00182 E.coli/Neisseria porin superfamily signature
94 104 InterPro IPR001702 Porin, Gram-negative type
151 162 PRINTS PR00182 E.coli/Neisseria porin superfamily signature
151 162 InterPro IPR001702 Porin, Gram-negative type
305 322 PRINTS PR00182 E.coli/Neisseria porin superfamily signature
305 322 InterPro IPR001702 Porin, Gram-negative type
52 63 PRINTS PR00182 E.coli/Neisseria porin superfamily signature
52 63 InterPro IPR001702 Porin, Gram-negative type
227 239 PRINTS PR00182 E.coli/Neisseria porin superfamily signature
227 239 InterPro IPR001702 Porin, Gram-negative type
17 21 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
1 21 SignalP_EUK SignalP-noTM SignalP-noTM
51 69 PRINTS PR00183 E.coli/Salmonella-type porin signature
51 69 InterPro IPR001897 Porin, gammaproteobacterial
94 116 PRINTS PR00183 E.coli/Salmonella-type porin signature
94 116 InterPro IPR001897 Porin, gammaproteobacterial
149 171 PRINTS PR00183 E.coli/Salmonella-type porin signature
149 171 InterPro IPR001897 Porin, gammaproteobacterial
261 280 PRINTS PR00183 E.coli/Salmonella-type porin signature
261 280 InterPro IPR001897 Porin, gammaproteobacterial
233 250 PRINTS PR00183 E.coli/Salmonella-type porin signature
233 250 InterPro IPR001897 Porin, gammaproteobacterial
22 38 PRINTS PR00183 E.coli/Salmonella-type porin signature
22 38 InterPro IPR001897 Porin, gammaproteobacterial
22 350 FunFam G3DSA:2.40.160.10:FF:000002 Outer membrane porin F
1 21 Phobius SIGNAL_PEPTIDE Signal peptide region
305 321 ProSitePatterns PS00576 General diffusion Gram-negative porins signature.
305 321 InterPro IPR013793 Porin, Gram-negative type, conserved site
22 350 Gene3D G3DSA:2.40.160.10 Porin
22 350 InterPro IPR023614 Porin domain superfamily
27 350 Pfam PF00267 Gram-negative porin
27 350 InterPro IPR001702 Porin, Gram-negative type
22 350 SUPERFAMILY SSF56935 Porins
1 350 PANTHER PTHR34501 PROTEIN YDDL-RELATED
1 4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 21 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
30 350 CDD cd00342 gram_neg_porins
30 350 InterPro IPR033900 Porin domain, Gram-negative type

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 · FPocket

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

Site 1 FPocket #3
0.996
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #8
0.513
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.679
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.65
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.637
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.317
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_A0A0H3GIV3
AlphaFold DB full sequence Viewing
ColabFold KP13_02140
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.

65 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 15 records from similar proteins
Structural ligands 15 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
451 PDB via homolog 417.5 Da · LogP 2.91 · TPSA 84.5 Open detail RCSB PDB
ASZ PDB via homolog Detail RCSB PDB
BOG PDB via homolog Detail RCSB PDB
C8E PDB via homolog Detail RCSB PDB
D10 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
451 RCSB PDB P02931 417.5 Da LogP 2.91 TPSA 84.5 ✓ Ro5 ✓ Clean CC(=O)Nc1ccc2c(c1)OCCOCCOc3ccccc3OCCOCCO2
ASZ RCSB PDB Q9K597 153.2 Da LogP -0.56 TPSA 57.6 ✓ Ro5 ✓ Clean CN(C)CCS(=O)(=O)O
BOG RCSB PDB P02931 292.4 Da LogP 0.16 TPSA 99.4 ✓ Ro5 ✓ Clean CCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1)CO)…
C8E RCSB PDB D6QLY1 306.4 Da LogP 2.41 TPSA 57.2 ✓ Ro5 ✓ Clean CCCCCCCCOCCOCCOCCOCCO
D10 RCSB PDB Q9K597 142.3 Da LogP 4.15 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCCCC
D12 RCSB PDB Q9K597 170.3 Da LogP 4.93 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCCCCCC
HEX RCSB PDB Q9K597 86.2 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCC
HP6 RCSB PDB Q9K597 100.2 Da LogP 2.98 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCC
LDA RCSB PDB D6QLY1 229.4 Da LogP 4.48 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCCC[N+](C)(C)[O-]
LMT RCSB PDB F2VN85 510.6 Da LogP -0.45 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](O1…
OCT RCSB PDB Q9K597 114.2 Da LogP 3.37 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCC
OES RCSB PDB Q9K597 206.4 Da LogP 2.09 TPSA 37.3 ✓ Ro5 ✓ Clean CCCCCCCC[S@@](=O)CCO
OLC RCSB PDB P02931 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)O
P6L RCSB PDB D6QLY1 747.0 Da LogP 10.22 TPSA 148.8 2 viol. ✓ Clean CCCCCCCCCC=CCCCCCCC(=O)OC[C@@H](CO[P@](=O)(O)OC…
QLB RCSB PDB P02931 262.4 Da LogP 2.39 TPSA 47.9 ✓ Ro5 ✓ Clean CCCCCCCCOCCOCCOCCO

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.