KpKP13 Protein target profile

Multidrug efflux pump KdeA

Accession: KP13_04269

Gene: AHE45499.1 kdeA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQD8
Length 410
Pocket druggability (P2Rank · AlphaFold DB model) 0.968
Direct ligand evidence 0 67 total records
Functional annotation 0 EC 7 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
1.9% 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
92.63 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) 0.968
Structure A0A0H3GQD8
Pocket Pocket 1
Druggability (FPocket) 0.969
Structure A0A0H3GQD8
Pocket Pocket 23
ColabFold model
P2Rank 0.955 · Pocket 1
FPocket 0.346 · Pocket 26
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 91 / 4744 genomes with a hit
Prevalence 1.9%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MQNYSLSGRRLGRQALLFPLCLVLYEFSTYIGNDMIQPGMLAVVQEFQVGNEWVPTSMTAYLAGGMFLQWLLGPLSDRIGRRPVMLTGVVWFIVTCLATLLAQTIEQFTLLRFLQGISLCFIGAVGYAAIQESFEEAVCIKITALMANVALIAPLLGPLVGAAWVHILPWEMMFVLFAVLAAISFFGLQRAMPETATRLGEKLSVKELGRDYRLVLKNLRFVAGALATGFVSLPLLAWIAQSPVIIISGEQATSYEYGMLQVPIFGALIAGNLVLARLTARRTVRSLIIMGGWPIMFGLILSAAATVVSSHAYLWMTAGLSFYAFGIGLANAGLVRLTLFASEMSKGTVSAAMGMLQMLIFTVGIELSKHAYELGGNGLFSLFNLLGGVLWLGLMIYFLKDKSVGNSQQG

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

7
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • 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:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • GO:0015385 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: Na+(out) + H+(in) = Na+(in) + H+(out).
  • GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
  • GO:1990961 A process that reduces or removes the toxicity of a xenobiotic by exporting it outside the cell.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

48 records
Show feature table
Start End DB Term Name
170 188 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
111 130 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
379 399 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
53 75 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 14 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
165 169 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
347 367 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
348 365 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
82 104 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
137 156 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
336 346 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
220 242 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
106 110 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
260 280 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
400 410 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
27 362 Pfam PF07690 Major Facilitator Superfamily
27 362 InterPro IPR011701 Major facilitator superfamily
15 33 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
219 240 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
189 218 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
34 52 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
14 405 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile.
14 405 InterPro IPR020846 Major facilitator superfamily domain
108 130 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
166 188 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
313 335 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
286 308 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
287 307 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
308 312 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
380 399 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
21 399 SUPERFAMILY SSF103473 MFS general substrate transporter
21 399 InterPro IPR036259 MFS transporter superfamily
73 83 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
257 279 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
313 335 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
131 141 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
53 72 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
142 164 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
72 88 ProSitePatterns PS00216 Sugar transport proteins signature 1.
72 88 InterPro IPR005829 Sugar transporter, conserved site
368 378 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
281 286 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
16 38 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
19 375 CDD cd17320 MFS_MdfA_MDR_like
84 105 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
19 396 PANTHER PTHR23502 MAJOR FACILITATOR SUPERFAMILY
241 259 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
20 397 Gene3D G3DSA:1.20.1720.10 Multidrug resistance protein D

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
0.968
Likely same site as FPocket 13 7.8 Å 30 shared residues 83% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.078
Likely same site as FPocket 23 3.0 Å 8 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.057
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Surrounding area
Pocket 4 P2Rank #4
0.037
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Surrounding area
Pocket 5 P2Rank #5
0.024
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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 #23
0.969 Unusual size
Likely same site as P2Rank 2 3.0 Å 8 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #12
0.625 Unusual size
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Surrounding area
Pocket 3 FPocket #13
0.262 Unusual size
Likely same site as P2Rank 1 7.8 Å 30 shared residues 83% 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_A0A0H3GQD8
AlphaFold DB full sequence Viewing
ColabFold KP13_04269
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.

67 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 17 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 13 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CLM PDB via homolog 323.1 Da · LogP 0.91 · TPSA 112.7 Open detail RCSB PDB
DXC PDB via homolog Detail RCSB PDB
KHJ PDB via homolog Detail RCSB PDB
LDA PDB via homolog Detail RCSB PDB
CHEMBL333888 ChEMBL via homolog · pchembl 6.52 (~302.0 nM) Detail ChEMBL

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
CLM RCSB PDB P0AEY8 323.1 Da LogP 0.91 TPSA 112.7 ✓ Ro5 ✓ Clean c1cc(ccc1[C@H]([C@@H](CO)NC(=O)C(Cl)Cl)O)[N+](=…
DXC RCSB PDB P0AEY8 392.6 Da LogP 4.48 TPSA 77.8 ✓ Ro5 ✓ Clean C[C@H](CCC(=O)O)[C@H]1CC[C@@H]2[C@@]1([C@H](C[C…
KHJ RCSB PDB P0AEY8 186.3 Da LogP 1.00 TPSA 7.8 ✓ Ro5 ✓ Clean C[n+]1ccc(cc1)c2cc[n+](cc2)C
LDA RCSB PDB P0AEY8 229.4 Da LogP 4.48 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCCC[N+](C)(C)[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.