KpATCC43816 Protein target profile

lipopolysaccharide export system ATP-binding protein lptB

Accession: VK055_3866

Gene: AIK82416.1 lptB 3D evidence: Experimental + AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A2X3II39
Length 241
Pocket druggability (P2Rank · AlphaFold DB model) 0.243
Direct ligand evidence 0 66 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
Hit
Human identity (%)
34.375 Lower values reduce human off-target concern.
Human E-value
1.03e-15
Gut microbiome similarity
26.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
96.68 Higher values support similarity to known essential genes.
DEG E-value
6.26e-172 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
94.86 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) 0.243
Structure A0A2X3II39
Pocket Pocket 1
Druggability (FPocket) 0.495
Structure A0A2X3II39
Pocket Pocket 1
ColabFold model
P2Rank 0.197 · Pocket 1
FPocket 0.316 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1254 / 4744 genomes with a hit
Prevalence 26.4%

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.

MATLTAKNLAKAYKGRRVVEDVSLTVNSGEIVGLLGPNGAGKTTTFYMVVGIVPRDAGNIIIDDEDISLLPLHARARRGIGYLPQEASIFRRLSVYDNLMAVLQIRDDLTSEQREDRAKELMEEFHIEHLRDSLGQALSGGERRRVEIARALAANPKFILLDEPFAGVDPISVIDIKRIIEHLRDSGLGVLITDHNVRETLAVCERAYIVSQGHLIAHGTPQQILEDEQVKRVYLGEDFRL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Cytoplasmic

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:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0055085 The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
20 166 Pfam PF00005 ABC transporter
20 166 InterPro IPR003439 ABC transporter-like, ATP-binding domain
3 241 NCBIfam TIGR04406 LPS export ABC transporter ATP-binding protein
3 241 InterPro IPR030921 LPS export ABC transporter, ATP-binding protein LptB
1 241 Gene3D G3DSA:3.40.50.300 -
1 241 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
2 240 PANTHER PTHR45772 CONSERVED COMPONENT OF ABC TRANSPORTER FOR NATURAL AMINO ACIDS-RELATED
1 241 FunFam G3DSA:3.40.50.300:FF:000151 Lipopolysaccharide ABC transporter ATP-binding protein
4 237 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
4 237 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
138 152 ProSitePatterns PS00211 ABC transporters family signature.
138 152 InterPro IPR017871 ABC transporter-like, conserved site
4 237 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
4 237 InterPro IPR003439 ABC transporter-like, ATP-binding domain
4 236 CDD cd03218 ABC_YhbG
4 236 InterPro IPR030921 LPS export ABC transporter, ATP-binding protein LptB
28 231 SMART SM00382 AAA_5
28 231 InterPro IPR003593 AAA+ ATPase domain
215 239 Pfam PF12399 Branched-chain amino acid ATP-binding cassette transporter
215 239 InterPro IPR032823 Branched-chain amino acid ATP-binding cassette transporter, C-terminal

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 #4
0.267
Show in viewer
Surrounding area
Pocket 2 P2Rank #6
0.124
Show in viewer
Surrounding area
Pocket 3 P2Rank #7
0.118
Show in viewer
Surrounding area
Pocket 4 P2Rank #8
0.076
Show in viewer
Surrounding area
Pocket 5 P2Rank #13
0.049
Show in viewer
Surrounding area
All structural evidence 1 experimental · 2 predicted

Structural evidence

1 + 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
PDB 7EFO
X-ray A Viewing
AlphaFold DB AF_A0A2X3II39
AlphaFold DB full sequence Loaded
ColabFold VK055_3866
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.

66 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 16 records from similar proteins
Structural ligands 16 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
AE3 PDB via homolog 134.2 Da · LogP 0.03 · TPSA 38.7 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
AOV PDB via homolog Detail RCSB PDB
CZJ PDB via homolog Detail RCSB PDB
DCQ 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
AE3 RCSB PDB O30650 134.2 Da LogP 0.03 TPSA 38.7 ✓ Ro5 ✓ Clean CCOCCOCCO
ANP RCSB PDB P0A9V4 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
AOV RCSB PDB P0A9V1 544.2 Da LogP -3.05 TPSA 299.4 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
CZJ RCSB PDB P0A9V1 586.6 Da LogP 3.32 TPSA 179.8 1 viol. ✓ Clean Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)C34CC5CC(C3)CC(C5…
DCQ RCSB PDB P0A9V4 322.4 Da LogP 4.49 TPSA 52.6 ✓ Ro5 Alert CCCCCCCCCCC1=C(C(=O)C(=C(C1=O)OC)OC)C
JU7 RCSB PDB O30650 346.5 Da LogP 1.33 TPSA 99.4 ✓ Ro5 ✓ Clean C1CCC(CC1)CCCCCCO[C@H]2[C@@H]([C@H]([C@@H]([C@H…
L0W RCSB PDB P0A9V4 1814.4 Da LogP 21.50 TPSA 394.5 4 viol. ✓ Clean CCCCCCCCCCCCCC(=O)O[C@H](CCCCCCCCCCC)CC(=O)O[C@…
LMD RCSB PDB P0A9V4 538.7 Da LogP 0.33 TPSA 178.5 3 viol. ✓ Clean CCCCCCCCCCCCCCO[C@H]1[C@@H]([C@H]([C@@H]([C@H](…
LMN RCSB PDB P0A9V4 1005.2 Da LogP -1.68 TPSA 357.1 3 viol. ✓ Clean CCCCCCCCCCC(CCCCCCCCCC)(CO[C@@H]1[C@@H]([C@@H](…
LMT RCSB PDB P0A9V4 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…
LPP RCSB PDB Q9HVW1 648.9 Da LogP 10.51 TPSA 119.4 2 viol. ✓ Clean CCCCCCCCCCCCCCCC(=O)OC[C@H](COP(=O)(O)O)OC(=O)C…
MA4 RCSB PDB O30650 508.6 Da LogP -0.84 TPSA 178.5 3 viol. ✓ Clean C1CCC(CC1)CCCCCCO[C@H]2[C@@H]([C@H]([C@@H]([C@H…
MMC RCSB PDB Q58663 215.6 Da LogP 0.58 TPSA 0.0 ✓ Ro5 ✓ Clean C[Hg+]
NOV RCSB PDB P0A9V1 612.6 Da LogP 3.63 TPSA 200.0 2 viol. ✓ Clean Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)c3ccc(c(c3)CC=C(C…
TBU RCSB PDB Q58663 74.1 Da LogP 0.78 TPSA 20.2 ✓ Ro5 ✓ Clean CC(C)(C)O
VO4 RCSB PDB A0A086HZU3 114.9 Da LogP -3.69 TPSA 86.2 ✓ Ro5 ✓ Clean [O-][V](=O)([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.

Structure