KpKP13 Protein target profile

Multidrug resistance protein mdtM

Accession: KP13_01752

Gene: AHE46524.1 mdtM 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GM13
Length 413
Pocket druggability (P2Rank · AlphaFold DB model) 0.953
Direct ligand evidence 0 67 total records
Functional annotation 0 EC 3 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
0.7% 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
91.41 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) 0.953
Structure A0A0H3GM13
Pocket Pocket 1
Druggability (FPocket) 0.716
Structure A0A0H3GM13
Pocket Pocket 26
ColabFold model
P2Rank 0.968 · Pocket 1
FPocket 0.978 · Pocket 15
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 33 / 4744 genomes with a hit
Prevalence 0.7%

Sequence

Primary amino-acid sequence viewer.

MMHRISHWLSRHAAALFFPAALILYDFSAYLTTDLIQPGILHVVRDFNADVALAPASVSLYMAGGMALQWLLGPLSDRIGRRPVLLTGALIFTLACLATLFTTSMTQFLIARFVQGTSICFIATVGYVTVQEAFEEKRSIRLMAVITSVVLVAPIVGPLSGAALMHFIHWKALFGIIAAMGLVAWLGLLLTMPETVRRGDVPFSPLGVLRDFRNVFRNRIFLLGAATLSLSYIPLMSWVAVSPVILMDAGGLTTSEFAWSQVPVFSAVIIANLSVARWVKDPTRPRFVLSAVPVQMLGLAILIVGNLVWPHVWLWSVLGTCFYAFGIGLIFPTLFRFTLFSNDLPKGTVSASLNIVILSVSALSIEGARWLWFHGGRLPFHLLAVAAGIVAACCLAGLLRHQRGQAVIEARQS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

3
  • 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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

50 records
Show feature table
Start End DB Term Name
72 89 ProSitePatterns PS00216 Sugar transport proteins signature 1.
72 89 InterPro IPR005829 Sugar transporter, conserved site
13 24 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
373 377 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 12 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
23 398 CDD cd17320 MFS_MdfA_MDR_like
104 108 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
27 355 Pfam PF07690 Major Facilitator Superfamily
27 355 InterPro IPR011701 Major facilitator superfamily
165 169 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
348 370 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
400 413 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
20 398 Gene3D G3DSA:1.20.1720.10 Multidrug resistance protein D
50 72 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
52 72 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
22 399 PANTHER PTHR23502 MAJOR FACILITATOR SUPERFAMILY
220 245 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
109 130 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
25 28 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
220 242 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
84 103 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
257 275 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
108 130 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
287 309 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
18 405 SUPERFAMILY SSF103473 MFS general substrate transporter
18 405 InterPro IPR036259 MFS transporter superfamily
142 164 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
191 219 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
29 51 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 28 Phobius SIGNAL_PEPTIDE Signal peptide region
380 399 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
73 83 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
246 256 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
313 335 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
276 286 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
12 413 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile.
12 413 InterPro IPR020846 Major facilitator superfamily domain
340 350 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
168 190 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.
142 164 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
257 275 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
287 309 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
310 314 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
351 372 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
84 103 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
170 190 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
315 339 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
378 399 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.

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

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.953
Likely same site as FPocket 26 2.8 Å 29 shared residues 94% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.417
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.046
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.031
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.025
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #26
0.716 Unusual size
Likely same site as P2Rank 1 2.8 Å 29 shared residues 94% 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_A0A0H3GM13
AlphaFold DB full sequence Viewing
ColabFold KP13_01752
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.

Cross-references

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