Protein target profile

KP13_04834

Outer membrane protein S1

Genome: KpKP13 Gene: ompS1 AHE43801.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVL2
Length 381
Pocket druggability 0.99
Direct ligand evidence 0 57 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
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
74.805 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
91.88 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 0.99
Structure A0A0H3GVL2
Pocket Pocket 7
P2Rank 0.732
Structure A0A0H3GVL2
Pocket Pocket 1
ColabFold model
FPocket 0.685 · Pocket 5
P2Rank 0.721 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 112 / 4744 genomes with a hit
Prevalence 2.4%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKRKVLALMVPALLMASAANAAEIYNKNGNKLDLYGKVDGLHYFSDDASEDGDQTYVRFGLKGETQITSELTGYGQWEYNIQANTSEKEGANSWTRLGFAGLKFADCGSLDYGRNYGVVYDIESWTDMLPEFGGDTYTQTDVYMTGRTNGVATYRNSDFFGLVDGLHFALQYQGNNENAGSGEGTNNGGKRKLARENGDGFGISSYYDLDMGISFGAAYSSSDRTHNQLAAARSSQRYANGDKADAWTVGAKYDANNIYLAAMYAETRNMTFYGNDSFGGIANKTQNFEVVAQYQFDDFNLPLRPSVAYLQSKGKDLYAYSRYGDKDLVKYVDVGMTYYFNKNMSTYVDYKINLLDEDDRFYKNSGIATDDIVALGLVYQF

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.

39 records
Show feature table
Start End DB Term Name
30 381 CDD cd00342 gram_neg_porins
30 381 InterPro IPR033900 Porin domain, Gram-negative type
5 16 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
22 38 PRINTS PR00183 E.coli/Salmonella-type porin signature
22 38 InterPro IPR001897 Porin, gammaproteobacterial
51 69 PRINTS PR00183 E.coli/Salmonella-type porin signature
51 69 InterPro IPR001897 Porin, gammaproteobacterial
282 301 PRINTS PR00183 E.coli/Salmonella-type porin signature
282 301 InterPro IPR001897 Porin, gammaproteobacterial
250 267 PRINTS PR00183 E.coli/Salmonella-type porin signature
250 267 InterPro IPR001897 Porin, gammaproteobacterial
95 117 PRINTS PR00183 E.coli/Salmonella-type porin signature
95 117 InterPro IPR001897 Porin, gammaproteobacterial
150 172 PRINTS PR00183 E.coli/Salmonella-type porin signature
150 172 InterPro IPR001897 Porin, gammaproteobacterial
1 21 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
1 381 PANTHER PTHR34501 PROTEIN YDDL-RELATED
17 21 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
22 381 SUPERFAMILY SSF56935 Porins
22 381 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 21 Phobius SIGNAL_PEPTIDE Signal peptide region
1 21 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
27 381 Pfam PF00267 Gram-negative porin
27 381 InterPro IPR001702 Porin, Gram-negative type
22 381 Gene3D G3DSA:2.40.160.10 Porin
22 381 InterPro IPR023614 Porin domain superfamily
332 348 ProSitePatterns PS00576 General diffusion Gram-negative porins signature.
332 348 InterPro IPR013793 Porin, Gram-negative type, conserved site
1 4 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
332 349 PRINTS PR00182 E.coli/Neisseria porin superfamily signature
332 349 InterPro IPR001702 Porin, Gram-negative type
244 256 PRINTS PR00182 E.coli/Neisseria porin superfamily signature
244 256 InterPro IPR001702 Porin, Gram-negative type
52 63 PRINTS PR00182 E.coli/Neisseria porin superfamily signature
52 63 InterPro IPR001702 Porin, Gram-negative type
152 163 PRINTS PR00182 E.coli/Neisseria porin superfamily signature
152 163 InterPro IPR001702 Porin, Gram-negative type
95 105 PRINTS PR00182 E.coli/Neisseria porin superfamily signature
95 105 InterPro IPR001702 Porin, 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 #7
0.99
Likely same site as P2Rank 1 3.4 Å 18 shared residues 69% of smaller site
Unusual size
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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.732
Likely same site as FPocket 7 3.4 Å 18 shared residues 69% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.419
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.215
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.201
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Surrounding area
Site 5 P2Rank #5
0.165
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_A0A0H3GVL2
AlphaFold DB full sequence Viewing
ColabFold KP13_04834
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.

57 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
C8E PDB via homolog 306.4 Da · LogP 2.41 · TPSA 57.2 Open detail RCSB PDB
D10 PDB via homolog Detail RCSB PDB
D12 PDB via homolog Detail RCSB PDB
HEX PDB via homolog Detail RCSB PDB
LDA 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
C8E RCSB PDB D6QLY0 306.4 Da LogP 2.41 TPSA 57.2 ✓ Ro5 ✓ Clean CCCCCCCCOCCOCCOCCOCCO
D10 RCSB PDB Q8CVW1 142.3 Da LogP 4.15 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCCCC
D12 RCSB PDB Q48473 170.3 Da LogP 4.93 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCCCCCCCC
HEX RCSB PDB Q8CVW1 86.2 Da LogP 2.59 TPSA 0.0 ✓ Ro5 ✓ Clean CCCCCC
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…
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…

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.