KpATCC43816 Protein target profile

dppA

Accession: VK055_3568

Gene: AIK82123.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GZX5
Length 526
Pocket druggability (P2Rank · AlphaFold DB model) 0.8
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 68 total records
Functional annotation 0 EC 5 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
No hit
Gut microbiome similarity
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
95.78 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) 0.8
Structure A0A0H3GZX5
Pocket Pocket 1
Druggability (FPocket) 0.687
Structure A0A0H3GZX5
Pocket Pocket 3
ColabFold model
P2Rank 0.798 · Pocket 1
FPocket 0.584 · Pocket 4
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 148 / 4744 genomes with a hit
Prevalence 3.1%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Catalyzed reaction

1 reaction 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.

MLKLGLSLVAMTVAASVQAKTLVYCSEGSPEGFNPQLFTSGTTYDASSVPIYNRLVEFKTGTTEVIPGLAEKWEVSADGKTYTFHLRQGVKWQDNKDFKPTRDLNADDVVFSFDRQKNTNNPYHKVSGGSYEYFEGMGLPDLISEVKKVDDNTVQFVLTRPEAPFLADLAMDFASILSKEYADNMLKAGTPEKVDLNPIGTGPFQLLQYQKDSRILYKAFPGYWGTKPKIDRLVFSITPDASVRYAKLQKNECQVMPYPNPADIARMKEDKNITLLEQPGLNVGYLSFNTEKKPLDDVKVRQALTYAVNKEAIIKAVYQGAGQAAKNLIPPTMWGYNDDVKDYTYDPEKAKQLLKEAGLEKGFTIDLWAMPVQRPYNPNARRMAEMIQADWAKIGVQAKIVTYEWGEYLKRAKAGEHQSVMMGWTGDNGDPDNFFATLFSCAAAKDGSNYSRWCYKPFEDLIQPARATDDHNKRIELYKQAQVVMHDQAPALIIAHSTVYEPVRKEVKGYVVDPLGKHHFDNVSVE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Periplasmic

Gene Ontology (GO)

5
  • GO:0043190 A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • 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:1904680 Enables the transfer of a peptide from one side of a membrane to the other.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records
Show feature table
Start End DB Term Name
1 19 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
202 287 FunFam G3DSA:3.40.190.10:FF:000036 Dipeptide ABC transporter, substrate-binding protein
41 201 Gene3D G3DSA:3.90.76.10 -
1 19 SignalP_EUK SignalP-noTM SignalP-noTM
12 526 PIRSF PIRSF002741 MppA
12 526 InterPro IPR030678 Peptide/nickel binding protein, MppA-type
41 201 FunFam G3DSA:3.90.76.10:FF:000002 Dipeptide ABC transporter, substrate-binding protein
283 501 FunFam G3DSA:3.10.105.10:FF:000002 Dipeptide ABC transporter, substrate-binding protein
15 19 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
283 501 Gene3D G3DSA:3.10.105.10 -
1 19 Phobius SIGNAL_PEPTIDE Signal peptide region
20 526 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
4 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
202 514 Gene3D G3DSA:3.40.190.10 -
13 522 PANTHER PTHR30290 PERIPLASMIC BINDING COMPONENT OF ABC TRANSPORTER
13 522 InterPro IPR039424 Solute-binding protein family 5
64 444 Pfam PF00496 Bacterial extracellular solute-binding proteins, family 5 Middle
64 444 InterPro IPR000914 Solute-binding protein family 5 domain
20 525 SUPERFAMILY SSF53850 Periplasmic binding protein-like II
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
21 510 CDD cd08493 PBP2_DppA_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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.8
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.782
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.061
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.018
Show in viewer
Surrounding area
Pocket 5 P2Rank #5
0.012
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #3
0.687
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_A0A0H3GZX5
AlphaFold DB full sequence Viewing
ColabFold VK055_3568
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.

68 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 18 records from similar proteins
Structural ligands 18 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
6RP PDB via homolog 192.2 Da · LogP 0.21 · TPSA 72.9 Open detail RCSB PDB
9YH PDB via homolog Detail RCSB PDB
9YK PDB via homolog Detail RCSB PDB
BHN PDB via homolog Detail RCSB PDB
BHR 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
6RP RCSB PDB P33590 192.2 Da LogP 0.21 TPSA 72.9 ✓ Ro5 ✓ Clean c1cnn(c1)C(C(=O)O)n2cccn2
9YH RCSB PDB P33590 448.5 Da LogP 2.60 TPSA 110.5 ✓ Ro5 Alert COc1cccc(c1O)CN(CCN(Cc2ccccc2SC)CC(=O)O)CC(=O)O
9YK RCSB PDB P33590 434.5 Da LogP 2.29 TPSA 121.5 ✓ Ro5 Alert CSc1ccccc1CN(CCN(Cc2cccc(c2O)O)CC(=O)O)CC(=O)O
BHN RCSB PDB P33590 388.4 Da LogP 1.57 TPSA 121.5 ✓ Ro5 Alert c1ccc(c(c1)C[N@@](CC[N@](Cc2ccccc2O)CC(=O)O)CC(…
BHR RCSB PDB P33590 404.4 Da LogP 1.28 TPSA 141.8 ✓ Ro5 Alert c1ccc(c(c1)C[N@@](CC[N@](Cc2cccc(c2O)O)CC(=O)O)…
BHZ RCSB PDB P33590 372.4 Da LogP 1.87 TPSA 101.3 ✓ Ro5 Alert c1ccc(cc1)C[N@@](CC[N@](Cc2ccccc2O)CC(=O)O)CC(=…
CMO RCSB PDB P33590 28.0 Da LogP -0.04 TPSA 19.9 ✓ Ro5 ✓ Clean [C-]#[O+]
DTD RCSB PDB P33590 152.2 Da LogP 0.10 TPSA 40.5 ✓ Ro5 ✓ Clean C1[C@@H]([C@H](CSS1)O)O
DTT RCSB PDB P33590 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
DTU RCSB PDB P33590 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@H]([C@H](CS)O)O)S
DTV RCSB PDB P33590 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@H]([C@@H](CS)O)O)S
EDT RCSB PDB P33590 292.2 Da LogP -2.07 TPSA 155.7 ✓ Ro5 ✓ Clean C(CN(CC(=O)O)CC(=O)O)N(CC(=O)O)CC(=O)O
G9Z RCSB PDB O50260 291.3 Da LogP -3.73 TPSA 158.8 1 viol. ✓ Clean C1=CC(=O)N([C@@H]1C(=O)O)C[C@H]([C@H]([C@@H]([C…
GDS RCSB PDB B8F653 612.6 Da LogP -3.88 TPSA 317.6 3 viol. ✓ Clean C(CC(=O)N[C@@H](CSSC[C@@H](C(=O)NCC(=O)O)NC(=O)…
HCT RCSB PDB P33590 190.2 Da LogP 0.03 TPSA 111.9 ✓ Ro5 ✓ Clean C(CC(=O)O)[C@H](CC(=O)O)C(=O)O
MLI RCSB PDB B8F653 102.0 Da LogP -3.12 TPSA 80.3 ✓ Ro5 ✓ Clean C(C(=O)[O-])C(=O)[O-]
OXL RCSB PDB Q0P844 88.0 Da LogP -3.51 TPSA 80.3 ✓ Ro5 ✓ Clean C(=O)(C(=O)[O-])[O-]
PER RCSB PDB P33590 32.0 Da LogP -2.38 TPSA 46.1 ✓ Ro5 ✓ Clean [O-][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.