KpKP13 Protein target profile

Maltose-binding periplasmic protein

Accession: KP13_00372

Gene: malE AHE46889.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GKX2
Length 396
Pocket druggability (P2Rank · AlphaFold DB model) 0.947
Direct ligand evidence 0 63 total records
Functional annotation 0 EC 8 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

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)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
93.64 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) 0.947
Structure A0A0H3GKX2
Pocket Pocket 1
Druggability (FPocket) 0.641
Structure A0A0H3GKX2
Pocket Pocket 1
ColabFold model
P2Rank 0.917 · Pocket 1
FPocket 0.611 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 112 / 4744 genomes with a hit
Prevalence 2.4%

Sequence

Primary amino-acid sequence viewer.

MKIKTGARILALSALTTMMFSASALAKIEEGKLVIWINGDKGYNGLAEVGKKFEKDTGIKVSVEHPDKLEEKFPQVAATGDGPDIIFWAHDRFGGYAQSGLLAEITPDKAFQDKLYPFTWDAVRYNGKLIAYPIAVEALSLIYNKDLVPNPPKTWEEIPALDKELKAKGKSALMFNLQEPYFTWPLIAADGGYAFKFENGKYDVKDVGVDSAGAKAGLTFLVDLIKNKHMNADTDYSIAEAAFNKGETAMTINGPWAWSNIDKSKVNYGVTLLPTFKGKPSKPFVGVLSAGINAASPNKELAKEFLENYLMTDQGLEAVNNDKPLGAVALKSFQEKLEKDPRIAATMANAQKGEIMPNIPQMSAFWYAVRTAVINAASGRQTVDAALKDAQSRITK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Subcellular localization

Localization
Periplasmic

Gene Ontology (GO)

8
  • GO:0008643 The directed movement of carbohydrate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Carbohydrates are a group of organic compounds based of the general formula Cx(H2O)y.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0015144 Enables the transfer of carbohydrate from one side of a membrane to the other.
  • GO:0055052 A complex for the transport of metabolites into the cell, consisting of 5 subunits: two ATP-binding subunits, two membrane spanning subunits, and one substrate-binding subunit. In organisms with two membranes, the substrate-binding protein moves freely in the periplasmic space and joins the other subunits only when bound with substrate. In organisms with only one membrane the substrate-binding protein is tethered to the cytoplasmic membrane and associated with the other subunits. Transport of the substrate across the membrane is driven by the hydrolysis of ATP.
  • 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:1901982 Binding to maltose.
  • GO:0042956 The directed movement of maltodextrin, any polysaccharide of glucose residues in beta-(1,4) linkage, across a membrane.
  • GO:0015768 The directed movement of maltose into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Maltose is the disaccharide 4-O-alpha-D-glucopyranosyl-D-glucopyranose, an intermediate in the catabolism of glycogen and starch.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
1 26 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
31 394 CDD cd13656 PBP2_MBP
133 150 ProSitePatterns PS01037 Bacterial extracellular solute-binding proteins, family 1 signature.
133 150 InterPro IPR006061 Solute-binding family 1, conserved site
9 17 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
1 8 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
45 309 Pfam PF01547 Bacterial extracellular solute-binding protein
45 309 InterPro IPR006059 Bacterial extracellular solute-binding protein
299 320 PRINTS PR00181 Maltose binding protein signature
299 320 InterPro IPR006060 Maltose/Cyclodextrin ABC transporter, substrate-binding protein
357 376 PRINTS PR00181 Maltose binding protein signature
357 376 InterPro IPR006060 Maltose/Cyclodextrin ABC transporter, substrate-binding protein
233 252 PRINTS PR00181 Maltose binding protein signature
233 252 InterPro IPR006060 Maltose/Cyclodextrin ABC transporter, substrate-binding protein
70 88 PRINTS PR00181 Maltose binding protein signature
70 88 InterPro IPR006060 Maltose/Cyclodextrin ABC transporter, substrate-binding protein
130 149 PRINTS PR00181 Maltose binding protein signature
130 149 InterPro IPR006060 Maltose/Cyclodextrin ABC transporter, substrate-binding protein
151 170 PRINTS PR00181 Maltose binding protein signature
151 170 InterPro IPR006060 Maltose/Cyclodextrin ABC transporter, substrate-binding protein
171 190 PRINTS PR00181 Maltose binding protein signature
171 190 InterPro IPR006060 Maltose/Cyclodextrin ABC transporter, substrate-binding protein
36 54 PRINTS PR00181 Maltose binding protein signature
36 54 InterPro IPR006060 Maltose/Cyclodextrin ABC transporter, substrate-binding protein
29 395 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
50 357 Gene3D G3DSA:3.40.190.10 -
1 26 Phobius SIGNAL_PEPTIDE Signal peptide region
27 396 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 24 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
138 388 Gene3D G3DSA:3.40.190.10 -
18 26 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
4 396 PANTHER PTHR30061 MALTOSE-BINDING PERIPLASMIC PROTEIN

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
0.947
Likely same site as FPocket 1 1.0 Å 22 shared residues 96% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.056
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Surrounding area
Pocket 3 P2Rank #3
0.046
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Surrounding area
Pocket 4 P2Rank #4
0.044
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Surrounding area
Pocket 5 P2Rank #5
0.022
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #1
0.641 Unusual size
Likely same site as P2Rank 1 1.0 Å 22 shared residues 96% of smaller site
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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_A0A0H3GKX2
AlphaFold DB full sequence Viewing
ColabFold KP13_00372
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.

63 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 13 records from similar proteins
Structural ligands 13 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
19H PDB via homolog 392.3 Da · LogP 5.80 · TPSA 62.3 Open detail RCSB PDB
3M6 PDB via homolog Detail RCSB PDB
3R4 PDB via homolog Detail RCSB PDB
3R6 PDB via homolog Detail RCSB PDB
3R7 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
19H RCSB PDB P0AEX9 392.3 Da LogP 5.80 TPSA 62.3 1 viol. Alert Cc1cc(cc(c1Cl)C)OCCCc2c3ccc(cc3[nH]c2C(=O)O)Cl
3M6 RCSB PDB P0AEY0 666.7 Da LogP 5.12 TPSA 145.3 2 viol. ✓ Clean C[C@@H]1CN(C(=O)c2cccc(c2O[C@@H]1CN(C)C(=O)Nc3c…
3R4 RCSB PDB P0AEX9 230.6 Da LogP 3.39 TPSA 37.3 ✓ Ro5 ✓ Clean c1cc2c(cc1F)sc(c2Cl)C(=O)O
3R6 RCSB PDB P0AEX9 184.2 Da LogP 1.81 TPSA 57.5 ✓ Ro5 ✓ Clean CSc1ccc(c(c1)C(=O)O)O
3R7 RCSB PDB P0AEX9 303.3 Da LogP 2.83 TPSA 83.5 ✓ Ro5 ✓ Clean C=Cc1ccc(c(c1)NS(=O)(=O)c2ccccc2)C(=O)O
865 RCSB PDB P0AEX9 628.7 Da LogP 5.49 TPSA 114.5 2 viol. Alert Cc1ccnc(c1c2cccc3c2n(c(c3CCCOc4cccc5c4cccc5)C(=…
B3P RCSB PDB P0AEX9 282.3 Da LogP -4.01 TPSA 145.4 1 viol. ✓ Clean C(CNC(CO)(CO)CO)CNC(CO)(CO)CO
LMT RCSB PDB P0AEX9 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…
P33 RCSB PDB Q2G1E9 326.4 Da LogP -0.93 TPSA 95.8 ✓ Ro5 ✓ Clean C(COCCOCCOCCOCCOCCOCCO)O
TMO RCSB PDB P0AEX9 75.1 Da LogP 0.19 TPSA 23.1 ✓ Ro5 ✓ Clean C[N+](C)(C)[O-]
TXT RCSB PDB B0B0V1 809.8 Da LogP -10.66 TPSA 400.3 3 viol. ✓ Clean C[C@@H]1[C@H]([C@H]([C@H]([C@H](O1)O[C@@H]2[C@H…
VCW RCSB PDB A9CEY9 318.3 Da LogP -3.95 TPSA 174.0 1 viol. ✓ Clean C([C@@H]1[C@H]([C@@H]([C@H]([C@H](O1)OC[C@@H](C…
XE RCSB PDB P0AEX9 131.3 Da LogP 0.00 TPSA 0.0 ✓ Ro5 ✓ Clean [Xe]

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.