KpKP13 Protein target profile

Outer membrane protein A

Accession: KP13_03871

Gene: ompA AHE45382.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GMF7
Length 379
Pocket druggability (P2Rank · AlphaFold DB model) 0.127
Direct ligand evidence 0 55 total records
Functional annotation 0 EC 6 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
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 (%)
83.989 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
74.7 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) 0.127
Structure A0A0H3GMF7
Pocket Pocket 1
Druggability (FPocket) 0.361
Structure A0A0H3GMF7
Pocket Pocket 4
ColabFold model
P2Rank 0.762 · Pocket 1
FPocket 0.664 · Pocket 5
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 111 / 4744 genomes with a hit
Prevalence 2.3%

Sequence

Primary amino-acid sequence viewer.

MKDLTVRSFVTSWRILDDNEAQKMKKTAIAIAVALAGFATVAQAAPKDNTWYAGGKLGWSQYHDTGFYGNGFQNNNGPTRNDQLGAGAFGGYQVNPYLGFEMGYDWLGRMAYKGSVDNGAFKAQGVQLTAKLGYPITDDLDIYTRLGGMVWRADSKGNYASTGVSRSEHDTGVSPVFAGGVEWAVTRDIATRLEYQWVNNIGDAGTVGTRPDNGMLSLGVSYRFGQEDAAPVVAPAPAPAPEVATKHFTLKSDVLFNFNKATLKPEGQQALDQLYTQLSNMDPKDGSAVVLGYTDRIGSEAYNQQLSEKRAQSVVDYLVAKGIPAGKISARGMGESNPVTGNTCDNVKARAALIDCLAPDRRVEIEVKGYKEVVTQPAA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
OuterMembrane

Gene Ontology (GO)

6
  • 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: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.
  • GO:0051701 An interaction between two organisms living together in more or less intimate association. The term host is used for the larger (macro) of the two members of a symbiosis; the various forms of symbiosis include parasitism, commensalism and mutualism.
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

48 records
Show feature table
Start End DB Term Name
1 27 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
1 44 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
243 371 ProSiteProfiles PS51123 OmpA-like domain profile.
243 371 InterPro IPR006665 OmpA-like domain
40 44 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
35 246 Gene3D G3DSA:2.40.160.20 -
255 350 Pfam PF00691 OmpA family
255 350 InterPro IPR006665 OmpA-like domain
35 246 FunFam G3DSA:2.40.160.20:FF:000003 Outer membrane protein A
253 367 CDD cd07185 OmpA_C-like
253 367 InterPro IPR006665 OmpA-like domain
45 379 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
24 371 Hamap MF_00842 Outer membrane protein A [ompA].
24 371 InterPro IPR002368 Outer membrane protein, OmpA
45 227 SUPERFAMILY SSF56925 OMPA-like
45 227 InterPro IPR011250 Outer membrane protein/outer membrane enzyme PagP, beta-barrel
288 303 PRINTS PR01021 OMPA domain signature
288 303 InterPro IPR006664 Outer membrane protein, bacterial
303 319 PRINTS PR01021 OMPA domain signature
303 319 InterPro IPR006664 Outer membrane protein, bacterial
256 278 PRINTS PR01021 OMPA domain signature
256 278 InterPro IPR006664 Outer membrane protein, bacterial
234 371 FunFam G3DSA:3.30.1330.60:FF:000004 Outer membrane protein A
247 365 PANTHER PTHR30329 STATOR ELEMENT OF FLAGELLAR MOTOR COMPLEX
46 227 Pfam PF01389 OmpA-like transmembrane domain
46 227 InterPro IPR000498 Outer membrane protein OmpA-like, transmembrane domain
290 334 ProSitePatterns PS01068 OmpA-like domain.
290 334 InterPro IPR006690 Outer membrane protein, OmpA-like, conserved site
28 39 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 44 Phobius SIGNAL_PEPTIDE Signal peptide region
247 369 Gene3D G3DSA:3.30.1330.60 -
247 369 InterPro IPR036737 OmpA-like domain superfamily
244 259 PRINTS PR01022 Outer membrane protein A signature
244 259 InterPro IPR002368 Outer membrane protein, OmpA
346 359 PRINTS PR01022 Outer membrane protein A signature
346 359 InterPro IPR002368 Outer membrane protein, OmpA
212 226 PRINTS PR01022 Outer membrane protein A signature
212 226 InterPro IPR002368 Outer membrane protein, OmpA
273 292 PRINTS PR01022 Outer membrane protein A signature
273 292 InterPro IPR002368 Outer membrane protein, OmpA
135 151 PRINTS PR01022 Outer membrane protein A signature
135 151 InterPro IPR002368 Outer membrane protein, OmpA
312 331 PRINTS PR01022 Outer membrane protein A signature
312 331 InterPro IPR002368 Outer membrane protein, OmpA
198 212 PRINTS PR01022 Outer membrane protein A signature
198 212 InterPro IPR002368 Outer membrane protein, OmpA
246 367 SUPERFAMILY SSF103088 OmpA-like
246 367 InterPro IPR036737 OmpA-like domain superfamily

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
0.127
Likely same site as FPocket 4 1.2 Å 12 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.003
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #4
0.361
Likely same site as P2Rank 1 1.2 Å 12 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #1
0.319
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_A0A0H3GMF7
AlphaFold DB full sequence Viewing
ColabFold KP13_03871
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.

55 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5GP PDB via homolog 363.2 Da · LogP -2.57 · TPSA 206.0 Open detail RCSB PDB
7QA PDB via homolog Detail RCSB PDB
API PDB via homolog Detail RCSB PDB
C8E PDB via homolog Detail RCSB PDB
SRT 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
5GP RCSB PDB Q9I4L6 363.2 Da LogP -2.57 TPSA 206.0 1 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=O)(O…
7QA RCSB PDB P13794 305.3 Da LogP -1.21 TPSA 179.0 1 viol. ✓ Clean C[C@H](C(=O)O)NC(=O)[C@H](CCC[C@H](C(=O)O)N)NC(…
API RCSB PDB Q6RYW5 190.2 Da LogP -1.02 TPSA 126.6 ✓ Ro5 ✓ Clean C(C[C@H](C(=O)O)N)C[C@@H](C(=O)O)N
C8E RCSB PDB P0A910 306.4 Da LogP 2.41 TPSA 57.2 ✓ Ro5 ✓ Clean CCCCCCCCOCCOCCOCCOCCO
SRT RCSB PDB Q6RYW5 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.

Cross-references

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