Protein target profile

VK055_2050

yjdL peptide transporter

Genome: KpATCC43816 Gene: AIK80656.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 6 reactions UniProt A0A0H3GKU2
Length 491
Pocket druggability 0.982
Metabolic reactions 6
Chokepoint No
Direct ligand evidence 0 64 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
Hit
Human identity (%)
31.658 Lower values reduce human off-target concern.
Human E-value
2.39e-17
Gut microbiome similarity
0.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
85.04 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 0.982
Structure A0A0H3GKU2
Pocket Pocket 10
P2Rank 0.934
Structure A0A0H3GKU2
Pocket Pocket 1
ColabFold model
FPocket 0.941 · Pocket 22
P2Rank 0.946 · Pocket 1
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.

Explore metabolic network
Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

6 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MKTPSQPRAIYYIVAIQIWEYFSFYGMRALLILYLTHQLGFDDSHAISLFSAYASLVYVTPILGGWLADRLLGNRTAVIAGALLMTLGHVVLGVESTSAWSLYVALAIIICGYGLFKSNISCLLGELYAHDDPRRDGGFSLLYAAGNVGSIAAPIACGLAAQWYGWHIGFALAGIGMFIGLMIFLSGSRHFRHTRGVDKPALRAVKFVLPTWGWLLVMLCLAPVFFTLLLQNNWSGYLLAIVCLFAAQMVARIMIKAPEHRRALWQIVLLMLAGTLFWVLAQQGGSSISLFIDHFVNRRLLNWDVPTALFQSVNAIAVMAAGVVLAWLMRPEGSVRSVLRVWLKFSFGLLLMGGGFMLLALNARHGAADGQASMGMMVAGLAMMGFAELFIDPVAMAQITRLNMPGVTGVLTGIYMLATGAVANWLAGVVAQQTTESQISDTAIAAYQHFFAQMGEWTLGCVAVMVIIAFAAACSVGKRRAAAGEITGGGA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • 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: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: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:0005886 The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
  • 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.

60 records
Show feature table
Start End DB Term Name
4 470 PANTHER PTHR23517 RESISTANCE PROTEIN MDTM, PUTATIVE-RELATED-RELATED
36 46 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
6 459 NCBIfam TIGR00924 oligopeptide:H+ symporter
6 459 InterPro IPR005279 Dipeptide/tripeptide permease
455 477 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
341 361 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
407 429 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
208 230 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
95 99 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
117 136 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
100 116 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
138 160 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
162 166 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 485 Gene3D G3DSA:1.20.1250.20 MFS general substrate transporter like domains
1 485 InterPro IPR036259 MFS transporter superfamily
308 329 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
103 125 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
229 233 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
71 93 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
234 251 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
167 186 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
7 470 CDD cd17346 MFS_DtpA_like
7 470 InterPro IPR005279 Dipeptide/tripeptide permease
234 251 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
47 68 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
46 68 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
396 406 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
1 192 ProSiteProfiles PS50850 Major facilitator superfamily (MFS) profile.
1 192 InterPro IPR020846 Major facilitator superfamily domain
252 262 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
477 491 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
428 456 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
341 363 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
75 94 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
12 35 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
76 440 Pfam PF00854 POT family
76 440 InterPro IPR000109 Proton-dependent oligopeptide transporter family
165 187 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
207 228 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
264 286 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
139 151 ProSitePatterns PS01023 PTR2 family proton/oligopeptide symporters signature 2.
139 151 InterPro IPR018456 PTR2 family proton/oligopeptide symporter, conserved site
407 427 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
69 74 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
306 328 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
373 395 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
187 206 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
282 307 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
373 395 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
362 372 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
330 340 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
457 476 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
4 476 SUPERFAMILY SSF103473 MFS general substrate transporter
4 476 InterPro IPR036259 MFS transporter superfamily
64 88 ProSitePatterns PS01022 PTR2 family proton/oligopeptide symporters signature 1.
64 88 InterPro IPR018456 PTR2 family proton/oligopeptide symporter, conserved site
9 31 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane.
137 161 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
263 281 Phobius TRANSMEMBRANE 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.

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 #10
0.982
Likely same site as P2Rank 2 1.1 Å 19 shared residues 90% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.934
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.75
Likely same site as FPocket 10 1.1 Å 19 shared residues 90% of smaller site
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.235
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Surrounding area
Site 4 P2Rank #4
0.231
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Surrounding area
Site 5 P2Rank #5
0.1
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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_A0A0H3GKU2
AlphaFold DB full sequence Viewing
ColabFold VK055_2050
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.