KpATCC43816 Protein target profile

periplasmic binding family protein

Accession: VK055_1926

Gene: AIK80532.1 fepB 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GL81
Length 319
Pocket druggability (P2Rank · AlphaFold DB model) 0.069
Direct ligand evidence 0 61 total records
Functional annotation 0 EC 2 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
1.7% 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.

Structure confidence

ColabFold pLDDT
91.37 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) 0.069
Structure A0A0H3GL81
Pocket Pocket 1
Druggability (FPocket) 0.382
Structure A0A0H3GL81
Pocket Pocket 1
ColabFold model
P2Rank 0.202 · Pocket 1
FPocket 0.479 · Pocket 8
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 81 / 4744 genomes with a hit
Prevalence 1.7%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MNFFSFCRRGALTGMLLLLGITSAQAADWPRQVTDSYGTHTLPSQPLRIVSTSVTLTGSLLAIDAPVVASGATTPNNRVADSQGFLRQWSEVAKARKLARLYIGEPSAEAVAAQMPDLILVSATGGDSALPLYDQLKTIAPTLVINYDDKSWQTLLTQLGQITGHEQQASARIADFNKQLVSLKEKMKLPPQPVTALVYTAAAHSANIWTPESAQGQMLEQLGFSLATLPGGLPASHSQGKRHDIVQLGGENLAAGLNGQSLFLFAGDQKDADAIYANPLLAHLPAVAGKRVYPLGTETFRLDYYSALLVLQRLSSLFG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization
Periplasmic

Gene Ontology (GO)

2
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • GO:1901678 The directed movement of an iron coordination entity into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
1 26 SignalP_EUK SignalP-noTM SignalP-noTM
146 318 FunFam G3DSA:3.40.50.1980:FF:000014 Ferrienterobactin-binding periplasmic protein FepB
27 319 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 26 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
166 186 Coils Coil Coil
27 145 FunFam G3DSA:3.40.50.1980:FF:000009 Iron-enterobactin transporter periplasmic binding protein
27 145 Gene3D G3DSA:3.40.50.1980 Nitrogenase molybdenum iron protein domain
1 9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
48 319 ProSiteProfiles PS50983 Iron siderophore/cobalamin periplasmic-binding domain profile.
48 319 InterPro IPR002491 ABC transporter periplasmic binding domain
44 313 CDD cd01146 FhuD
22 26 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
49 296 Pfam PF01497 Periplasmic binding protein
49 296 InterPro IPR002491 ABC transporter periplasmic binding domain
31 315 SUPERFAMILY SSF53807 Helical backbone metal receptor
1 26 Phobius SIGNAL_PEPTIDE Signal peptide region
10 21 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
17 314 PANTHER PTHR30532 IRON III DICITRATE-BINDING PERIPLASMIC PROTEIN
146 319 Gene3D G3DSA:3.40.50.1980 Nitrogenase molybdenum iron protein domain

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

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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
0.069
Likely same site as FPocket 1 2.0 Å 9 shared residues 90% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.068
Likely same site as FPocket 1 6.8 Å 6 shared residues 60% of smaller site
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
0.382
Likely same site as P2Rank 1 2.0 Å 9 shared residues 90% of smaller site
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_A0A0H3GL81
AlphaFold DB full sequence Viewing
ColabFold VK055_1926
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.

61 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 11 records from similar proteins
Structural ligands 11 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
5LC PDB via homolog 374.4 Da · LogP 1.84 · TPSA 139.1 Open detail RCSB PDB
7PG PDB via homolog Detail RCSB PDB
8LC PDB via homolog Detail RCSB PDB
95B PDB via homolog Detail RCSB PDB
9RT 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
5LC RCSB PDB Q0P8Q4 374.4 Da LogP 1.84 TPSA 139.1 1 viol. Alert c1cc(c(c(c1)O)O)C(=O)NCCCCCNC(=O)c2cccc(c2O)O
7PG RCSB PDB A0A2P5JFB2 384.5 Da LogP -0.26 TPSA 94.1 ✓ Ro5 ✓ Clean COCCOCCOCCOCCOCCOCCOCCOCCO
8LC RCSB PDB Q0P8Q4 416.5 Da LogP 3.01 TPSA 139.1 1 viol. Alert c1cc(c(c(c1)O)O)C(=O)NCCCCCCCCNC(=O)c2cccc(c2O)O
95B RCSB PDB Q0P8Q4 418.4 Da LogP 1.29 TPSA 176.4 1 viol. Alert c1cc(c(c(c1)O)O)C(=O)NCCCC[C@@H](C(=O)O)NC(=O)c…
9RT RCSB PDB Q0P8Q4 277.3 Da LogP 1.02 TPSA 85.1 ✓ Ro5 ✓ Clean c1ccnc(c1)CNS(=O)(=O)c2ccc(cc2)CN
DBS RCSB PDB Q0P8Q4 241.2 Da LogP -0.73 TPSA 127.1 ✓ Ro5 Alert c1cc(c(c(c1)O)O)C(=O)N[C@@H](CO)C(=O)O
EB4 RCSB PDB P0AEL6 669.6 Da LogP -0.74 TPSA 287.6 3 viol. Alert c1cc(c(c(c1)O)O)C(=O)N[C@H]2COC(=O)[C@H](COC(=O…
EHS RCSB PDB Q0P8Q4 464.4 Da LogP -0.97 TPSA 222.9 1 viol. Alert c1cc(c(c(c1)O)O)C(=O)N[C@@H](CO)C(=O)OC[C@@H](C…
LCM RCSB PDB Q0P8Q4 360.4 Da LogP 1.45 TPSA 139.1 1 viol. Alert c1cc(c(c(c1)O)O)C(=O)NCCCCNC(=O)c2cccc(c2O)O
PXJ RCSB PDB Q0P8Q4 388.4 Da LogP 2.23 TPSA 139.1 1 viol. Alert c1cc(c(c(c1)O)O)C(=O)NCCCCCCNC(=O)c2cccc(c2O)O
VBN RCSB PDB Q9RCF6 705.7 Da LogP 1.84 TPSA 243.1 3 viol. Alert C[C@@H]1[C@H](N=C(O1)c2cccc(c2O)O)C(=O)NCCCN(CC…

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.