Protein target profile

KP13_00142

Inner membrane symporter

Genome: KpKP13 Gene: AHE42062.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3H4M0
Length 464
Pocket druggability 0.744
Direct ligand evidence 0 52 total records
Functional annotation 0 EC 6 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
Hit
Human identity (%)
30.247 Lower values reduce human off-target concern.
Human E-value
4.49e-10
Gut microbiome similarity
1.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
44.444 Higher values support similarity to known essential genes.
DEG E-value
2.03e-121 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
88.12 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 0.744
Structure A0A0H3H4M0
Pocket Pocket 22
P2Rank 0.964
Structure A0A0H3H4M0
Pocket Pocket 1
ColabFold model
FPocket 0.966 · Pocket 26
P2Rank 0.97 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 54 / 4744 genomes with a hit
Prevalence 1.1%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKDHILSVKEKIGYGMGDAASHIIFDNVMLYMMFFYTDIFGIPAGFVGTMFLLARALDAISDPCMGLLADRTRSRWGKFRPWILFGAIPFGLVCVLAYSSPDLSHNGKLIYAAVTYTLLTLLYTVVNIPYCALGGVITDNPTQRISLQSWRFVLATAGGMLSTVLMMPLVNFIGGEDKALGFQGGIAVLSVIAFLMLAFCFFTTKERVEAPPSSTSMREDLRDIWRNDQWRVVGVLTILNILAVCVRGGAMMYYTTWIMGSAALFTAFLTTYCVGNLIGSALAKPLTDWKCKVSVFWWTNALLAVLSVAMFFVPMDAEITMFVFIFVIGVLHQLVTPIQWVMMSDTVDYGEWCNGKRLTGISFAGTLFVLKLGLALGGALIGWMLAGGGYDAAAKTQNSATLTIIIALFTLVPAVCYLLSAVIAKRYYTLKTPFLKKMMAELAEGARRNEQDFTAAPIDKEWQN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0015293 Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy.
  • GO:0006814 The directed movement of sodium ions (Na+) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0022857 Enables the transfer of a substance, usually a specific substance or a group of related substances, from one side of a membrane to the other.
  • 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:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

49 records
Show feature table
Start End DB Term Name
203 231 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
79 98 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
295 313 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
59 78 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
319 342 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
16 421 FunFam G3DSA:1.20.1250.20:FF:000045 Glycoside-pentoside-hexuronide family transporter
152 174 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
258 280 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
109 131 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
404 428 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
13 421 SUPERFAMILY SSF103473 MFS general substrate transporter
13 421 InterPro IPR036259 MFS transporter superfamily
260 283 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
82 99 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
293 315 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
429 464 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
255 259 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
363 384 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
232 254 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
314 318 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
175 179 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
12 34 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
363 385 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
13 427 Pfam PF13347 MFS/sugar transport protein
11 431 CDD cd17332 MFS_MelB_like
19 424 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains
19 424 InterPro IPR036259 MFS transporter superfamily
11 443 NCBIfam TIGR00792 glycoside-pentoside-hexuronide (GPH):cation symporter
11 443 InterPro IPR001927 Sodium:galactoside symporter
320 342 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
133 151 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
400 422 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 11 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
99 109 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
284 294 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
152 174 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
232 254 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
110 132 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
343 362 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
40 58 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
62 87 ProSitePatterns PS00872 Sodium:galactoside symporter family signature.
62 87 InterPro IPR018043 Sodium:galactoside symporter, conserved site
385 403 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
180 202 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
179 201 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
35 39 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
32 54 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
2 446 PANTHER PTHR11328 MAJOR FACILITATOR SUPERFAMILY DOMAIN-CONTAINING PROTEIN
2 446 InterPro IPR039672 Lactose permease-like

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 #22
0.744
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Surrounding area
Site 2 FPocket #7
0.702
Likely same site as P2Rank 1 5.3 Å 21 shared residues 81% of smaller site
Unusual size
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Surrounding area
Site 3 FPocket #29
0.658
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Surrounding area
Site 4 FPocket #30
0.617
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
0.964
Likely same site as FPocket 7 5.3 Å 21 shared residues 81% of smaller site
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Surrounding area
Site 2 P2Rank #2
0.186
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Surrounding area
Site 3 P2Rank #3
0.154
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Surrounding area
Site 4 P2Rank #4
0.044
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Surrounding area
Site 5 P2Rank #5
0.04
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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_A0A0H3H4M0
AlphaFold DB full sequence Viewing
ColabFold KP13_00142
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.

52 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
9PG PDB via homolog 301.3 Da · LogP -1.23 · TPSA 142.5 Open detail RCSB PDB
LMO PDB via homolog Detail RCSB PDB
ZINC1070097 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC12359987 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC12359988 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

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
9PG RCSB PDB P30878 301.3 Da LogP -1.23 TPSA 142.5 ✓ Ro5 ✓ Clean c1cc(ccc1[N+](=O)[O-])O[C@@H]2[C@@H]([C@H]([C@H…
LMO RCSB PDB P30878 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…

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.