KpATCC43816 Protein target profile

exported protein required for envelope biosynthesis and integrity

Accession: VK055_2523

Gene: AIK81120.1 lptD 3D evidence: Experimental + ColabFold model Metabolism Not in network UniProt C4T9I0
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Length 740
Pocket druggability (P2Rank · Experimental) 0.875
Direct ligand evidence 1 53 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.

Main supporting evidence

Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Direct ligand evidence 1 direct ligand records. Strong known ligand: co-crystal structure 1 PDB record(s) show a ligand actually co-crystallized with this exact protein - real experimental evidence, not a computational prediction. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Review the complete evidence below

Risks to review

Microbiome similarity 112 of 4744 screened genomes (2.4%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.88) — check the ligand evidence before deprioritizing on off-target risk alone. Mixed conservation Core/accessory calls are not fully concordant.

Evidence coverage

Core evidence streams are available for this target.
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
2.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
81.586 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
93.23 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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) 0.875
Structure 5IV8
Pocket Pocket 1
Druggability (FPocket) 0.656
Structure 5IV8
Pocket Pocket 20
ColabFold model
P2Rank 0.906 · Pocket 1
FPocket 0.962 · Pocket 63
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 112 / 4744 genomes with a hit
Prevalence 2.4%

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.

MEGRPGDLPVTINADHAKGNYPDNAVFTGNVDINQGNSRLRADEVQLHQQQAAGQAQPVRTVDALGNVHYDDNQVILKGPKAWSNLNTKDTNVWQGDYQMVGRQGRGTADLMKQRGENRYTILENGSFTSCLPGSDTWSVVGSEVIHDREEQVAEIWNARFKLGSVPIFYSPYLQLPVGDKRRSGFLIPNAKYSTKNGVEFSLPYYWNIAPNFDATITPHYMNKRGGVMWENEFRYLTQLGSGLTEFDYLPSDKVYEDDHSSDSNSRRWLFYWNHSGVIDQVWRLNADYTKVSDPDYFNDFSSKYGSSTDGYATQKFSAGYVNQNFDATVSTKQFQVFDRESSNSYSAEPQLDVNYYQNDVGPFDTHLYGQVAHFVNSNNNMPEATRVHFEPTINLPLSNGWGSLNTEAKLLATHYQQSNLDKYNAANGTDYKESVSRVMPQFKVDGKMVFERDLQEGFTQTLEPRVQYLYVPYRDQSEIGNYDSTLLQSDYTGLFRDRTYSGLDRIASANQVTTGLTSRVYDAAAVERFNISVGQIYYFTESRTGDDNINWENNDTTGSLVWAGDTYWRIADEWGLRGGIQYDTRLDNVATGNGTIEYRRDENRLVQLNYRYASPEYIQATLPSYSTAAQYKQGISQVGMTASWPIVDRWSVVGAYYYDTNTRKAANQMLGVQYNSCCYAIRLGYERKVNGWNSNDNGGESKYDNTFGINIELRGLSSNYGLGTQQMLRSNILPYQSSL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

7 GO

Subcellular localization

Localization
OuterMembrane

Gene Ontology (GO)

7
  • GO:0019867 The external membrane of Gram-negative bacteria or certain organelles such as mitochondria and chloroplasts; freely permeable to most ions and metabolites.
  • GO:0009279 A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • GO:0061024 A process which results in the assembly, arrangement of constituent parts, or disassembly of a membrane. A membrane is a double layer of lipid molecules that encloses all cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins.
  • GO:0015920 The directed movement of lipopolysaccharides into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. A lipopolysaccharide is any of a group of related, structurally complex components of the outer membrane of Gram-negative bacteria. Lipopolysaccharides consist three covalently linked regions, lipid A, core oligosaccharide, and an O side chain. Lipid A is responsible for the toxicity of the lipopolysaccharide.
  • GO:0010033 OBSOLETE. 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 organic substance stimulus.
  • GO:0043165 The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.
  • GO:1990351 A protein complex facilitating transport of molecules (proteins, small molecules, nucleic acids) into, out of or within a cell, or between cells.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

8 records
Show feature table
Start End DB Term Name
7 719 Hamap MF_01411 LPS-assembly protein LptD [lptD].
7 719 InterPro IPR020889 LPS-assembly protein LptD
6 160 Gene3D G3DSA:2.60.450.10 Lipopolysaccharide (LPS) transport protein A like domain
267 651 Pfam PF04453 LPS transport system D
267 651 InterPro IPR007543 LptD, C-terminal
11 152 Pfam PF03968 LptA/(LptD N-terminal domain) LPS transport protein
11 152 InterPro IPR005653 Organic solvent tolerance-like, N-terminal
6 736 PANTHER PTHR30189 LPS-ASSEMBLY PROTEIN

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
0.948
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Surrounding area
Pocket 2 P2Rank #2
0.918
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Surrounding area
Pocket 3 P2Rank #3
0.909
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Surrounding area
Pocket 4 P2Rank #4
0.802
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Surrounding area
Pocket 5 P2Rank #5
0.736
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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 #38
0.92
Show in viewer
Surrounding area
All structural evidence 2 experimental · 1 predicted

Structural evidence

2 + 1

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
PDB 5IV9
X-ray 4.37 Å A
96.8% 25-740
PDBe RCSB PDBj File
Viewing
PDB 5IV8
X-ray 2.94 Å A,C
72.7% 203-740
PDBe RCSB PDBj File
Loaded
ColabFold VK055_2523
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 1 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 3 1 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
C8E PDB co-crystal 306.4 Da · LogP 2.41 · TPSA 57.2 Open detail RCSB PDB
CAC PDB via homolog Detail RCSB PDB
LDA PDB via homolog Detail RCSB PDB
ZINC100014200 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC100070166 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
C8E RCSB PDB
5IV9 4.37 Å Open crystal
306.4 Da LogP 2.41 TPSA 57.2 ✓ Ro5 ✓ Clean CCCCCCCCOCCOCCOCCOCCO

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.

Sequence

UniProt C4T9I0

Structure

PDB 5IV9 PDB 5IV8