Protein target profile

KP13_05551

Periplasmic binding protein/LacI transcriptional regulator family protein

Genome: KpKP13 Gene: AHE44557.1 3D evidence: Experimental + ColabFold model UniProt A6T990

Export view

Length 317

Pocket druggability 0.5

Direct ligand evidence 0 53 total records

Functional annotation 0 EC 0 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.

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. No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Moderate predicted binding pocket FPocket selected-pocket score 0.50. This supports review but is not experimental validation. Structure available Experimental + ColabFold model Review the complete evidence below

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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: 0.2% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Localization

Localization: Unknown

Structure confidence

ColabFold pLDDT: 92.55 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.5

Structure 5HSG

Pocket Pocket 3

P2Rank 0.156

Structure 5HSG

Pocket Pocket 1

ColabFold model

FPocket 0.305 · Pocket 8

P2Rank 0.149 · Pocket 1

Core conservation Accessory gene

Roary accessory

CoreCruncher accessory

Gut microbiome 10 / 4744 genomes with a hit

Prevalence 0.2%

Cross-references

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

Sequence

UniProt A6T990

Structure

PDB 5HSG

Sequence

Primary amino-acid sequence viewer.

MMLFHTGKLRLLAVATTMLASMSFISAASAAGPTYALVQINQQALFFNLMNKGAQDAAKASGKDLVIFNSNDNPVAQNDAIENYIQQGVKGILVAAIDVNGIMPAVKEAAAANIPVIAIDAVLPAGPQAAQVGVDNIEGGRIIGQYFVDYVQKEMGGQARLGIVGALNSAIQNQRQKGFEETLKSNPKITIANVVDGQNVQDKAMTAAENLITGNPDLTAIYATGEPALLGAIAAVENQGRQKDIKVFGWDLTAKAISGIDGGYVTAVLQQDPEKMGAEALNALNSITSGKTVPKTILVPATVVTKANVDSYRPLFK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

No GO or EC annotations are currently loaded for this protein.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
1	30	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
1	30	Phobius	SIGNAL_PEPTIDE	Signal peptide region
31	317	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	10	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
133	309	Gene3D	G3DSA:3.40.50.2300	-
23	30	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	30	SignalP_EUK	SignalP-noTM	SignalP-noTM
33	312	SUPERFAMILY	SSF53822	Periplasmic binding protein-like I
33	312	InterPro	IPR028082	Periplasmic binding protein-like I
11	22	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
34	313	CDD	cd06317	PBP1_ABC_sugar_binding-like
51	297	Gene3D	G3DSA:3.40.50.2300	-
13	312	PANTHER	PTHR46847	D-ALLOSE-BINDING PERIPLASMIC PROTEIN-RELATED
43	291	Pfam	PF13407	Periplasmic binding protein domain
43	291	InterPro	IPR025997	Periplasmic binding 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.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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 #3

0.5

Show in viewer

Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.156

Show in viewer

Surrounding area

Site 2 P2Rank #2

0.019

Show in viewer

Surrounding area

All structural evidence 1 experimental · 1 predicted

Structural evidence

1 + 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 5HSG	X-ray	—	A	—	PDBe RCSB PDBj File	Viewing
ColabFold KP13_05551	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 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 3 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

BDR PDB via homolog 150.1 Da · LogP -2.58 · TPSA 90.2 Open detail RCSB PDB

GZL PDB via homolog Detail RCSB PDB

RIP PDB via homolog Detail RCSB PDB

ZINC15657695 ZINC proposed compound · Tanimoto 0.955 Detail ZINC

ZINC25721048 ZINC proposed compound · Tanimoto 0.955 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
BDR RCSB PDB	3KSM	Q2S7D2	150.1 Da LogP -2.58 TPSA 90.2	✓ Ro5	✓ Clean	`C([C@@H]1[C@H]([C@H]([C@@H](O1)O)O)O)O`
GZL RCSB PDB	2VK2	P39325	180.2 Da LogP -3.22 TPSA 110.4	✓ Ro5	✓ Clean	`C(C([C@H]1C(C([C@@H](O1)O)O)O)O)O`
RIP RCSB PDB	4ZJP	A6VKT0	150.1 Da LogP -2.58 TPSA 90.2	✓ Ro5	✓ Clean	`C1[C@H]([C@H]([C@H]([C@@H](O1)O)O)O)O`

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
ZINC15657695 ZINC	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@@…`
ZINC25721048 ZINC	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H]1O[C@@H](O)[C@H](O)[C@@H](O)[C…`
ZINC25721054 ZINC	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H]1O[C@H](O)[C@H](O)[C@@H](O)[C@…`
ZINC4726901 ZINC	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@H](O)[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C@…`
ZINC4726902 ZINC	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C…`
ZINC4726903 ZINC	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@H](O)[C@@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[C…`
ZINC4726904 ZINC	0.955	210.2 Da LogP -3.86 TPSA 130.6	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H]1O[C@@H](O)[C@@H](O)[C@@H](O)[…`
ZINC4403098 ZINC	0.630	240.2 Da LogP -4.50 TPSA 150.8	1 viol.	✓ Clean	`OC[C@H](O)[C@H](O)[C@H]1O[C@@H](O)[C@@H](O)[C@@…`
ZINC4403099 ZINC	0.630	240.2 Da LogP -4.50 TPSA 150.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@H](O)[C@H]1O[C@@H](O)[C@@H](O)[C@…`
ZINC4403100 ZINC	0.630	240.2 Da LogP -4.50 TPSA 150.8	1 viol.	✓ Clean	`OC[C@H](O)[C@@H](O)[C@H]1O[C@@H](O)[C@@H](O)[C@…`
ZINC4403101 ZINC	0.630	240.2 Da LogP -4.50 TPSA 150.8	1 viol.	✓ Clean	`OC[C@@H](O)[C@@H](O)[C@H]1O[C@@H](O)[C@@H](O)[C…`
ZINC104251170 ZINC	0.600	207.2 Da LogP -2.65 TPSA 93.4	✓ Ro5	✓ Clean	`CN(C)[C@@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC203488208 ZINC	0.600	207.2 Da LogP -2.65 TPSA 93.4	✓ Ro5	✓ Clean	`CN(C)[C@@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC257346191 ZINC	0.600	207.2 Da LogP -2.65 TPSA 93.4	✓ Ro5	✓ Clean	`CN(C)[C@H]1[C@H](O)[C@@H](O)[C@@H](CO)O[C@H]1O`
ZINC257346192 ZINC	0.600	207.2 Da LogP -2.65 TPSA 93.4	✓ Ro5	✓ Clean	`CN(C)[C@H]1[C@H](O)[C@H](O)[C@@H](CO)O[C@H]1O`
ZINC12953172 ZINC	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](OC[C@H]2O[C@@H](O)[C@H](O)[C@@H…`
ZINC12953178 ZINC	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](OC[C@H]2O[C@H](O)[C@H](O)[C@@H]…`
ZINC13543637 ZINC	0.593	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]…`
ZINC13544387 ZINC	0.593	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@@…`
ZINC13544561 ZINC	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@H]2O[C@@H](O)[C@@H](O)[C@@H…`
ZINC16051576 ZINC	0.593	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…`
ZINC1857777749 ZINC	0.593	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…`
ZINC2382416917 ZINC	0.593	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	0.593	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@@…`
ZINC2382416920 ZINC	0.593	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…`
ZINC2383776696 ZINC	0.593	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	0.593	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…`
ZINC2383776699 ZINC	0.593	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@@…`
ZINC238808850 ZINC	0.593	666.6 Da LogP -9.75 TPSA 347.8	3 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@H]2O[C@H](OC[C@H]3O[C@H](OC…`
ZINC238808929 ZINC	0.593	828.7 Da LogP -11.92 TPSA 427.0	3 viol.	✓ Clean	`OC[C@H]1O[C@H](O[C@@H]2[C@@H](CO)O[C@H](O[C@@H]…`
ZINC238809271 ZINC	0.593	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]…`
ZINC238809273 ZINC	0.593	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]…`
ZINC245204569 ZINC	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](OC[C@@H]2O[C@H](O)[C@H](O)[C@H]…`
ZINC253615788 ZINC	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](OC[C@@H]2O[C@H](O)[C@@H](O)[C@H…`
ZINC35262676 ZINC	0.593	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@@…`
ZINC3830983 ZINC	0.593	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	0.593	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	0.593	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	0.593	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]…`
ZINC4095711 ZINC	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@H]2O[C@H](O)[C@@H](O)[C@@H]…`
ZINC4096704 ZINC	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@H]2O[C@H](O)[C@H](O)[C@@H](…`
ZINC4228251 ZINC	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@H](OC[C@H]2O[C@H](O)[C@H](O)[C@@H](…`
ZINC4261772 ZINC	0.593	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	0.593	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…`
ZINC575127216 ZINC	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](OC[C@@H]2O[C@H](O)[C@@H](O)[C@@…`
ZINC575127217 ZINC	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@@H]1O[C@H](OC[C@@H]2O[C@H](O)[C@@H](O)[C@@…`
ZINC599389315 ZINC	0.593	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]…`
ZINC64219263 ZINC	0.593	342.3 Da LogP -5.40 TPSA 189.5	2 viol.	✓ Clean	`OC[C@H]1O[C@@H](OC[C@H]2O[C@@H](O)[C@@H](O)[C@@…`
ZINC72283167 ZINC	0.593	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]…`
ZINC958527474 ZINC	0.593	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.