Protein target profile

KP13_03783

O-antigen export system ATP-binding protein rfbB

Genome: KpKP13 Gene: rfbB AHE43682.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GV79
Length 246
Pocket druggability 0.881
Direct ligand evidence 0 58 total records
Functional annotation 0 EC 4 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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 (%)
33.493 Lower values reduce human off-target concern.
Human E-value
5.68e-26
Gut microbiome similarity
1.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
41.736 Higher values support similarity to known essential genes.
DEG E-value
1.43e-64 Smaller values mean stronger essential-gene similarity.

Localization

Localization
CytoplasmicMembrane

Structure confidence

ColabFold pLDDT
90.47 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 0.881
Structure A0A0H3GV79
Pocket Pocket 17
P2Rank 0.155
Structure A0A0H3GV79
Pocket Pocket 1
ColabFold model
FPocket 0.986 · Pocket 3
P2Rank 0.277 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 54 / 4744 genomes with a hit
Prevalence 1.1%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MHPVINFSHVTKEYPLYHHIGSGIKDLIFHPKRAFQLLKGRKYLAIEDVSFTVGKGEAVALIGRNGAGKSTSLGLVAGVIKPTKGTVTTEGRVASMLELGGGFHPELTGRENIYLNATLLGLRRKEVQQRMERIIEFSELGEFIDEPIRVYSSGMLAKLGFSVISQVEPDILIIDEVLAVGDIAFQAKCIQTIRDFKKRGVTILFVSHNMSDVEKICDRVIWIENHRLREVGPADRIIELYKQAMA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0016020 A lipid bilayer along with all the proteins and protein complexes embedded in it and attached to it.
  • 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:0140359 Primary active transporter characterized by two nucleotide-binding domains and two transmembrane domains. Uses the energy generated from ATP hydrolysis to drive the transport of a substance across a membrane.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
55 244 SMART SM00382 AAA_5
55 244 InterPro IPR003593 AAA+ ATPase domain
47 177 Pfam PF00005 ABC transporter
47 177 InterPro IPR003439 ABC transporter-like, ATP-binding domain
5 232 CDD cd03220 ABC_KpsT_Wzt
5 232 InterPro IPR015860 ABC transporter, teichoic acids export TagH-like
151 165 ProSitePatterns PS00211 ABC transporters family signature.
151 165 InterPro IPR017871 ABC transporter-like, conserved site
1 246 Gene3D G3DSA:3.40.50.300 -
1 246 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
42 239 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
42 239 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 245 PANTHER PTHR46743 TEICHOIC ACIDS EXPORT ATP-BINDING PROTEIN TAGH
22 246 ProSiteProfiles PS50893 ATP-binding cassette, ABC transporter-type domain profile.
22 246 InterPro IPR003439 ABC transporter-like, ATP-binding domain

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 #17
0.881
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
0.155
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.013
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.004
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_A0A0H3GV79
AlphaFold DB full sequence Viewing
ColabFold KP13_03783
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.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2BA PDB via homolog 658.4 Da · LogP -1.63 · TPSA 309.7 Open detail RCSB PDB
ANP PDB via homolog Detail RCSB PDB
BET PDB via homolog Detail RCSB PDB
LDA PDB via homolog Detail RCSB PDB
NH4 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
2BA RCSB PDB Q9KIF7 658.4 Da LogP -1.63 TPSA 309.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@H]4[C@H](O3)C…
ANP RCSB PDB Q97UY8 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)…
BET RCSB PDB Q9KIF7 118.2 Da LogP -0.22 TPSA 37.3 ✓ Ro5 ✓ Clean C[N+](C)(C)CC(=O)O
LDA RCSB PDB O67181 229.4 Da LogP 4.48 TPSA 23.1 ✓ Ro5 ✓ Clean CCCCCCCCCCCC[N+](C)(C)[O-]
NH4 RCSB PDB Q9YGA6 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
P4G RCSB PDB O67181 162.2 Da LogP 1.08 TPSA 27.7 ✓ Ro5 ✓ Clean CCOCCOCCOCC
PE5 RCSB PDB O67181 398.5 Da LogP 0.13 TPSA 94.1 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOCCOCCOCCOCCO
POP RCSB PDB O57933 176.0 Da LogP -2.08 TPSA 129.9 ✓ Ro5 ✓ Clean O[P@@](=O)([O-])O[P@@](=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.