Genome KpATCC43816

Protein target profile

dipeptide permease D

Accession: VK055_1812

Gene: AIK80424.1 dtpD 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GQ97
Length 492
Pocket druggability (P2Rank) 0.952
Direct ligand evidence 0 64 total records
Functional annotation 0 EC 11 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 (%)
32.692 Lower values reduce human off-target concern.
Human E-value
5.600000000000001e-23
Gut microbiome similarity
0.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
87.3 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) 0.952
Structure A0A0H3GQ97
Pocket Pocket 1
Druggability (FPocket) 0.985
Structure A0A0H3GQ97
Pocket Pocket 2
ColabFold model
P2Rank 0.953 · Pocket 1
FPocket 0.727 · Pocket 31
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 42 / 4744 genomes with a hit
Prevalence 0.9%

Cross-references

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

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.

MQTTSSQPRAIYYVVALQIWEYFSFYGMRALLILYLTNQLKYDDNHAYALFSAYCSLVYVTPILGGYLADKLLGNRMAVMLGALLMAIGHLVLGASETAPLFLYLSLAIIVCGYGLFKSNVSCLLGELYEPADPRRDGGFSLMYAAGNIGSIIAPIACGYVQEEYSWAMGFALAAIGMVAGLVIFLCGNRHFQHTAGVNRQALCARRFLLPNWGWLLVLLVTAPLLIAVLFWQEWSVYALIVATAIGLAVLARIYLRAETDKQRKDLRLIVVLTAFSLLFWAFAQQGGSSISLYIDRFVNRHIMSYEVPTAMFQSINAFAVMLCGMVLAWLVKESVNGNRTVRIWGKFALGLGLMSAGFCILTLSARWSAAYGQSSMPLMVLGLAVMGFAELFIDPVAMSQITRIEIPGVTGVLTGIYMLLSGAIANYLAGVIADQTSQASFDAAGAVNYSIDAYITVFSQITWGALACVGVVLVIWLYHSLKVRTRRLAVE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

11 GO

Subcellular localization

Localization
CytoplasmicMembrane

Gene Ontology (GO)

11
  • GO:1904680 Enables the transfer of a peptide from one side of a membrane to the other.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • 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:0006857 The directed movement of oligopeptides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Oligopeptides are molecules that contain a small number (2 to 20) of amino-acid residues connected by peptide linkages.
  • GO:0015833 The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • 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:0042938 The directed movement of a dipeptide, a combination of two amino acids by means of a peptide (-CO-NH-) link, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
  • GO:0071916 Enables the transfer of a dipeptide from one side of a membrane to the other. A dipeptide is a combination of two amino acids linked together by a peptide (-CO-NH-) bond.
  • GO:0015333 Enables the transfer of a solute or solutes from one side of a membrane to the other according to the reaction: peptide(out) + H+(out) = peptide(in) + H+(in), up its concentration gradient. The transporter binds the solute and undergoes a series of conformational changes. Transport works equally well in either direction and is driven by hydrogen ion movement.
  • GO:0015031 The directed movement of proteins 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.

65 records
Show feature table
Start End DB Term Name
311 332 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
188 207 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
366 376 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
410 432 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
140 152 ProSitePatterns PS01023 PTR2 family proton/oligopeptide symporters signature 2.
140 152 InterPro IPR018456 PTR2 family proton/oligopeptide symporter, conserved site
65 89 ProSitePatterns PS01022 PTR2 family proton/oligopeptide symporters signature 1.
65 89 InterPro IPR018456 PTR2 family proton/oligopeptide symporter, conserved site
13 35 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
48 69 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
45 67 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 492 FunFam G3DSA:1.20.1250.20:FF:000035 Dipeptide permease D
410 434 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
12 36 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
8 477 CDD cd17346 MFS_DtpA_like
8 477 InterPro IPR005279 Dipeptide/tripeptide permease
138 162 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
77 443 Pfam PF00854 POT family
77 443 InterPro IPR000109 Proton-dependent oligopeptide transporter family
167 189 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
232 236 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
10 483 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile.
10 483 InterPro IPR020846 Major facilitator superfamily domain
5 189 SUPERFAMILY SSF103473 MFS general substrate transporter
5 189 InterPro IPR036259 MFS transporter superfamily
70 75 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
101 117 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
344 365 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
399 409 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
454 479 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
98 117 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
1 492 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains
1 492 InterPro IPR036259 MFS transporter superfamily
72 94 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
168 187 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
344 366 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
480 492 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
376 398 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
285 310 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
377 398 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
267 284 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
256 266 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
210 232 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
208 231 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
237 255 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
435 453 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
96 100 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
118 137 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
2 483 PANTHER PTHR23517 RESISTANCE PROTEIN MDTM, PUTATIVE-RELATED-RELATED
163 167 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
37 47 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
333 343 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
76 95 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
208 480 SUPERFAMILY SSF103473 MFS general substrate transporter
208 480 InterPro IPR036259 MFS transporter superfamily
1 492 Hamap MF_01880 Dipeptide permease D [dtpD].
1 492 InterPro IPR023777 Amino acid/peptide transporter family, dipeptide permease D
269 288 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
457 479 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
237 256 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
310 332 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.
138 157 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
6 464 NCBIfam TIGR00924 oligopeptide:H+ symporter
6 464 InterPro IPR005279 Dipeptide/tripeptide permease

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

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.952
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Surrounding area
Pocket 2 P2Rank #2
0.656
Likely same site as FPocket 2 3.6 Å 16 shared residues 76% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.13
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Surrounding area
Pocket 4 P2Rank #4
0.114
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Surrounding area
Pocket 5 P2Rank #5
0.032
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2
0.985 Unusual size
Likely same site as P2Rank 2 3.6 Å 16 shared residues 76% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #36
0.296
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_A0A0H3GQ97
AlphaFold DB full sequence Viewing
ColabFold VK055_1812
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.

64 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 14 records from similar proteins
Structural ligands 14 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
78M PDB via homolog 314.5 Da · LogP 3.75 · TPSA 66.8 Open detail RCSB PDB
78N PDB via homolog Detail RCSB PDB
97M PDB via homolog Detail RCSB PDB
97N PDB via homolog Detail RCSB PDB
AFS 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
78M RCSB PDB Q5M4H8 314.5 Da LogP 3.75 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCC/C=C\CCCCCC(=O)OC[C@H](CO)O
78N RCSB PDB Q5M4H8 314.5 Da LogP 3.75 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCC/C=C\CCCCCC(=O)OC[C@@H](CO)O
97M RCSB PDB Q5M4H8 328.5 Da LogP 4.14 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCC/C=C\CCCCCCCC(=O)OC[C@@H](CO)O
97N RCSB PDB Q5M4H8 328.5 Da LogP 4.14 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCC/C=C\CCCCCCCC(=O)OC[C@H](CO)O
AFS RCSB PDB Q8EHE6 196.1 Da LogP -1.03 TPSA 112.7 ✓ Ro5 ✓ Clean C[C@@H](C(=O)N[C@@H](C)P(=O)(O)O)N
F9E RCSB PDB P77304 354.4 Da LogP -1.44 TPSA 171.4 ✓ Ro5 ✓ Clean CC(C)[C@@H](C(=O)OC[C@H](CO)OCn1cnc2c1NC(=NC2=O…
LMT RCSB PDB P77304 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…
OLA RCSB PDB Q5KYD1 282.5 Da LogP 6.11 TPSA 37.3 1 viol. ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)O
OLB RCSB PDB Q5KYD1 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC/C=C\CCCCCCCC(=O)OC[C@H](CO)O
OLC RCSB PDB Q5KYD1 356.5 Da LogP 4.92 TPSA 66.8 ✓ Ro5 ✓ Clean CCCCCCCC\C=C/CCCCCCCC(=O)OC[C@@H](CO)O
OPK RCSB PDB A0A2R9TD79 424.5 Da LogP 1.54 TPSA 173.9 ✓ Ro5 ✓ Clean CC(C)[C@@H](C(=O)O)NC(=O)[C@H](CCCCNC(=O)OCc1cc…
PE5 RCSB PDB Q5M4H8 398.5 Da LogP 0.13 TPSA 94.1 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCOCCO
PG0 RCSB PDB Q5M4H8 120.1 Da LogP -0.36 TPSA 38.7 ✓ Ro5 ✓ Clean COCCOCCO
UMQ RCSB PDB A0A2R9TD79 496.6 Da LogP -0.84 TPSA 178.5 2 viol. ✓ Clean CCCCCCCCCCCO[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.