KpATCC43816 Protein target profile

bacterial extracellular solute-binding family protein

Accession: VK055_4265

Gene: AIK82810.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GX53

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Length 428

Pocket druggability (P2Rank · AlphaFold DB model) 0.949

Direct ligand evidence 0 51 total records

Functional annotation 0 EC 1 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.

Main supporting evidence

Risks to review

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: 0.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 26.923 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT: 94.04 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) 0.949

Structure A0A0H3GX53

Pocket Pocket 1

Druggability (FPocket) 0.363

Structure A0A0H3GX53

Pocket Pocket 6

ColabFold model

P2Rank 0.95 · Pocket 1

FPocket 0.99 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 42 / 4744 genomes with a hit

Prevalence 0.9%

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.

MKNVLISATLSATLGLSAFSSLAQDVDLRMSWWGGNGRHQVTLKALEEFHKQHPDINVKAEYTGWDGHLSRLTTQIAGGTEPDVMQTNWNWLPIFSKNGDGFYDLNTLKDEIDLSQFDAKELQSTTVNGKLNGIPISVTARVFYFNDEAWKKAGIPFPKTWDELMAAGKTFESKLGKQYYPVVLEHQDVLALLNSYMVQKYNQPAIDEKGRKFSYSKAQWADFFGMYKKLIDSHVMPDTRYYASFGKSNMYEMKPWIQGEWGGTYMWNSTINKYSDNLKPPAKLVLGEYPMLPGATDAGLFFKPAQMLSIGKSTKNPQAAAKVINFLLNSKEGVDILGLERGVPLSKAAVTYLTEDGVIKADDPAVSGLKLAQSLPTALPVSPYFDDPQIVAQFGTTLQYIDYGKKSVEEAAEDFQRQTDRILRRAMR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Subcellular localization

Localization: Unknown

Gene Ontology (GO)

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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

13 records

Show feature table

Start	End	DB	Term	Name
24	423	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
4	15	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	23	Phobius	SIGNAL_PEPTIDE	Signal peptide region
4	344	PANTHER	PTHR43649	ARABINOSE-BINDING PROTEIN-RELATED
137	415	Gene3D	G3DSA:3.40.190.10	-
1	23	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
16	23	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
45	331	Pfam	PF01547	Bacterial extracellular solute-binding protein
45	331	InterPro	IPR006059	Bacterial extracellular solute-binding protein
28	371	Gene3D	G3DSA:3.40.190.10	-
24	428	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	3	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	23	SignalP_GRAM_NEGATIVE	SignalP-noTM	SignalP-noTM

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

0.949

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Surrounding area

Pocket 2 P2Rank #2

0.241

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Surrounding area

Pocket 3 P2Rank #3

0.071

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Surrounding area

Pocket 4 P2Rank #4

0.034

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Surrounding area

Pocket 5 P2Rank #5

0.009

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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 #6

0.363

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Surrounding area

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.95

Likely same site as FPocket 1 1.7 Å 36 shared residues 84% of smaller site

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Surrounding area

Pocket 2 P2Rank #2

0.218

Likely same site as FPocket 20 2.2 Å 11 shared residues 100% of smaller site

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Surrounding area

Pocket 3 P2Rank #3

0.013

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Surrounding area

Pocket 4 P2Rank #4

0.009

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Surrounding area

Pocket 5 P2Rank #5

0.008

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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 #1

0.99 Unusual size

Likely same site as P2Rank 1 1.7 Å 36 shared residues 84% of smaller site

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Surrounding area

Pocket 2 FPocket #20

0.722

Likely same site as P2Rank 2 2.2 Å 11 shared residues 100% of smaller site

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Surrounding area

Pocket 3 FPocket #2

0.303

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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_A0A0H3GX53	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_4265	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.

51 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

TXT PDB via homolog 809.8 Da · LogP -10.66 · TPSA 400.3 Open detail RCSB PDB

ZINC100055151 ZINC proposed compound · Tanimoto 0.569 Detail ZINC

ZINC100055153 ZINC proposed compound · Tanimoto 0.569 Detail ZINC

ZINC100055156 ZINC proposed compound · Tanimoto 0.569 Detail ZINC

ZINC100055157 ZINC proposed compound · Tanimoto 0.569 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.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
TXT RCSB PDB	3K02	B0B0V1	809.8 Da LogP -10.66 TPSA 400.3	3 viol.	✓ Clean	`C[C@@H]1[C@H]([C@H]([C@H]([C@H](O1)O[C@@H]2[C@H…`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC100055151 ZINC	0.569	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@H](O[C@H]2[C@H](O[C@@H]3[C@@H](CO)O…`
ZINC100055153 ZINC	0.569	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@H](O[C@H]2[C@H](O[C@@H]3[C@@H](CO)O…`
ZINC100055156 ZINC	0.569	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](CO)O[C@@H…`
ZINC100055157 ZINC	0.569	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@H](O[C@H]2[C@@H](O)[C@@H](CO)O[C@@H…`
ZINC2362797719 ZINC	0.569	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@@H](O[C@H]2[C@H](O[C@H]3[C@@H](O)[C…`
ZINC55537584 ZINC	0.569	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@@H](O[C@H]2[C@H](O[C@@H]3[C@@H](CO)…`
ZINC103664702 ZINC	0.549	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@@H](O)O[C@H…`
ZINC103664705 ZINC	0.549	488.4 Da LogP -6.55 TPSA 248.4	2 viol.	✓ Clean	`C[C@@H]1O[C@@H](O[C@@H]2[C@@H](O)[C@H](O)O[C@H]…`
ZINC100352116 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@H…`
ZINC12358840 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@@H]2[C@@H](CO)O[C@H](O)[C@H…`
ZINC13542690 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@H](O)[C@@H…`
ZINC13543637 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@H]1O[C@H]…`
ZINC13544017 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@H]2[C@@H](CO)O[C@H](O)[C@H](…`
ZINC13544387 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O)[C@@…`
ZINC13549339 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@H]1O[C@@H…`
ZINC16051576 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@H]2[C@@H](CO)O[C@@H](O)[C@H…`
ZINC169619623 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@@H]1O[C@H…`
ZINC1857777749 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@H…`
ZINC1857777750 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O[C@…`
ZINC202563257 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@H…`
ZINC21984931 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O)[C@@H](O)[C@@H](O)[C@@H]1O[C@@…`
ZINC2382416917 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@@H]2[C@H](CO)O[C@@H](O)[C@@…`
ZINC2382416919 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@@H]2[C@H](CO)O[C@@H](O)[C@@…`
ZINC2383776696 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O[C@H]2[C@H](CO)O[C@@H](O)[C@H…`
ZINC2383776697 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O[C@H]2[C@H](CO)O[C@@H](O)[C@H…`
ZINC238735529 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@@H]1O[C@…`
ZINC238809271 ZINC	0.532	990.9 Da LogP -14.10 TPSA 506.1	3 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@H](O[C@@H]…`
ZINC242495944 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@H]…`
ZINC257362198 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@H]…`
ZINC257362199 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@H]…`
ZINC26892042 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@@H]1O[C@…`
ZINC35262676 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@…`
ZINC35262677 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@…`
ZINC3830982 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@H…`
ZINC3830983 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@H…`
ZINC3830985 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O[C@@H]2[C@H](CO)O[C@H](O)[C@H…`
ZINC38599727 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O[C@@H]2[C@H](CO)O[C@H](O)[C@H]…`
ZINC38599730 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@H]…`
ZINC38599734 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@H]…`
ZINC38792149 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](O[C@H]2[C@@H](CO)O[C@H](O)[C@H]…`
ZINC4095490 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@H](O)[C@H]…`
ZINC4095762 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@@H](O)[C@H…`
ZINC4261771 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@…`
ZINC4261772 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@…`
ZINC44185569 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@@H…`
ZINC5222455 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@@H](O)[C@H](O)[C@H]1O[C@H]…`
ZINC5222464 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O)[C@@H](O)[C@H](O)[C@H]1O[C@H…`
ZINC599389315 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@@H](O)[C@H](O)[C@H](O)[C@H]1O[C@H]…`
ZINC72283166 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@H]…`
ZINC72283167 ZINC	0.532	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](O)[C@H](O)[C@H](O)[C@@H]1O[C@H]…`

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 A0A0H3GX53