KpKP13 Protein target profile

Leucine-specific-binding protein

Accession: KP13_09592

Gene: livK ANJ86568.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GZM8

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Length 369

Pocket druggability (P2Rank · AlphaFold DB model) 0.079

Direct ligand evidence 0 51 total records

Functional annotation 0 EC 3 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

Microbiome similarity 120 of 4744 screened genomes (2.5%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.39. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.08.

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: 2.5% 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.

Structure confidence

ColabFold pLDDT: 94.65 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) 0.079

Structure A0A0H3GZM8

Pocket Pocket 1

Druggability (FPocket) 0.385

Structure A0A0H3GZM8

Pocket Pocket 4

ColabFold model

P2Rank 0.125 · Pocket 1

FPocket 0.184 · Pocket 16

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 120 / 4744 genomes with a hit

Prevalence 2.5%

Sequence

Primary amino-acid sequence viewer.

MKRNAKTIVAGIVALAMSHAAMAKDIKVAVVGAMSGPVAQWGDMEFNGARQAIKDINASGGIKGDKLVAVEYDDACDPKQAVAVANKIVNDGIQYVIGHLCSSSTQPASDIYEDEGILMISPGATNPELTQRGYQYIMRTAGLDSSQGPTAAKYIVEKVKPQRIAIIHDKQQYGEGLARSVQDNLKKAGANIVFFDGITAGEKDFSALLARLKKENIDFVYYGGYYPEMGQMLRQARSVGLKTVFMGPEGVGNASLSNIAGAAAEGMLVTMPKRYDQDPANSAIVNALKAEKKDPSGPYVWITYAAVQSLAQAMDRTGSQQPLDLIKDLKAHGAKTVIGPLTWDEKGDLKGFEFGVFQWHADGSSSAAK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization: Periplasmic

Gene Ontology (GO)

GO:0006865 The directed movement of amino acids, organic acids containing one or more amino substituents, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
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.
GO:0015820 The directed movement of L-leucine, 2-amino-4-methylpentanoic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

30 records

Show feature table

Start	End	DB	Term	Name
1	23	SignalP_EUK	SignalP-noTM	SignalP-noTM
1	23	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
144	272	FunFam	G3DSA:3.40.50.2300:FF:000033	Amino acid ABC transporter substrate-binding protein
27	343	Gene3D	G3DSA:3.40.50.2300	-
1	23	Phobius	SIGNAL_PEPTIDE	Signal peptide region
3	368	PANTHER	PTHR47151	LEU/ILE/VAL-BINDING ABC TRANSPORTER SUBUNIT
24	363	SUPERFAMILY	SSF53822	Periplasmic binding protein-like I
24	363	InterPro	IPR028082	Periplasmic binding protein-like I
1	6	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
24	369	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
27	359	CDD	cd06342	PBP1_ABC_LIVBP-like
16	23	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
26	363	Pfam	PF13458	Periplasmic binding protein
26	363	InterPro	IPR028081	Leucine-binding protein domain
7	15	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
144	272	Gene3D	G3DSA:3.40.50.2300	-
26	42	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
26	42	InterPro	IPR000709	Leu/Ile/Val-binding protein
254	272	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
254	272	InterPro	IPR000709	Leu/Ile/Val-binding protein
329	344	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
329	344	InterPro	IPR000709	Leu/Ile/Val-binding protein
67	85	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
67	85	InterPro	IPR000709	Leu/Ile/Val-binding protein
48	64	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
48	64	InterPro	IPR000709	Leu/Ile/Val-binding protein
277	290	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
277	290	InterPro	IPR000709	Leu/Ile/Val-binding protein
88	98	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
88	98	InterPro	IPR000709	Leu/Ile/Val-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.

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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

0.079

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Surrounding area

Pocket 2 P2Rank #2

0.04

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Surrounding area

Pocket 3 P2Rank #3

0.01

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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 #4

0.385

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Surrounding area

Pocket 2 FPocket #16

0.316

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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

0.125

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Surrounding area

Pocket 2 P2Rank #2

0.038

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Surrounding area

Pocket 3 P2Rank #3

0.026

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Surrounding area

Pocket 4 P2Rank #4

0.006

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Surrounding area

Pocket 5 P2Rank #5

0.002

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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_A0A0H3GZM8	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_09592	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

ABU PDB via homolog 103.1 Da · LogP -0.19 · TPSA 63.3 Open detail RCSB PDB

ZINC13357569 ZINC proposed compound · Tanimoto 0.778 Detail ZINC

ZINC1763117 ZINC proposed compound · Tanimoto 0.778 Detail ZINC

ZINC1845814 ZINC proposed compound · Tanimoto 0.778 Detail ZINC

ZINC22048354 ZINC proposed compound · Tanimoto 0.778 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
ABU RCSB PDB	3IP9	Q7CX36	103.1 Da LogP -0.19 TPSA 63.3	✓ Ro5	✓ Clean	`C(CC(=O)O)CN`

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
ZINC13357569 ZINC	0.778	243.4 Da LogP 3.71 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCC(=O)O`
ZINC1763117 ZINC	0.778	201.3 Da LogP 2.54 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCC(=O)O`
ZINC1845814 ZINC	0.778	215.3 Da LogP 2.93 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCC(=O)O`
ZINC22048354 ZINC	0.778	229.4 Da LogP 3.32 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCC(=O)O`
ZINC34552398 ZINC	0.778	257.4 Da LogP 4.10 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCC(=O)O`
ZINC34628306 ZINC	0.778	271.4 Da LogP 4.49 TPSA 63.3	✓ Ro5	✓ Clean	`NCCCCCCCCCCCCCCCC(=O)O`
ZINC3074822 ZINC	0.667	229.3 Da LogP 2.11 TPSA 80.4	✓ Ro5	✓ Clean	`NCCCCCC(=O)CCCCCC(=O)O`
ZINC4822737 ZINC	0.667	313.5 Da LogP 4.45 TPSA 80.4	✓ Ro5	✓ Clean	`NCCCCCCCCCCCC(=O)CCCCCC(=O)O`
ZINC1569727 ZINC	0.593	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](C)C(=O)O`
ZINC1569728 ZINC	0.593	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@@H](C)C(=O)O`
ZINC1569729 ZINC	0.593	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](C)C(=O)O`
ZINC1569730 ZINC	0.593	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@H](C)C(=O)O`
ZINC1529497 ZINC	0.588	230.3 Da LogP 3.06 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCC(=O)O`
ZINC1531045 ZINC	0.588	202.2 Da LogP 2.28 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCC(=O)O`
ZINC1593115 ZINC	0.588	216.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCC(=O)O`
ZINC1700020 ZINC	0.588	244.3 Da LogP 3.45 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCC(=O)O`
ZINC3860440 ZINC	0.588	258.4 Da LogP 3.84 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCC(=O)O`
ZINC3861298 ZINC	0.588	286.4 Da LogP 4.62 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCCC(=O)O`
ZINC5113062 ZINC	0.588	272.4 Da LogP 4.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)CCCCCCCCCCCCCC(=O)O`
ZINC2522597 ZINC	0.586	246.3 Da LogP -0.60 TPSA 129.7	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)C[C@H](N)C(=O)O)C(=O)O`
ZINC40470158 ZINC	0.577	216.3 Da LogP 0.49 TPSA 92.4	✓ Ro5	✓ Clean	`NCCCC(=O)NCCCCCC(=O)O`
ZINC1532219 ZINC	0.571	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](CC(C)C)C(=O)O`
ZINC1532220 ZINC	0.571	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)[C@H](N)CC(C)C)C(=O)O`
ZINC1532221 ZINC	0.571	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](CC(C)C)C(=O)O`
ZINC1532222 ZINC	0.571	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@H](CC(C)C)C(=O)O`
ZINC64219359 ZINC	0.565	202.3 Da LogP -0.41 TPSA 106.4	✓ Ro5	✓ Clean	`CC(C)[C@H](C(=O)[C@@H](C)N)[C@H](N)C(=O)O`
ZINC64219360 ZINC	0.565	202.3 Da LogP -0.41 TPSA 106.4	✓ Ro5	✓ Clean	`CC(C)[C@@H](C(=O)[C@@H](C)N)[C@H](N)C(=O)O`
ZINC78311249 ZINC	0.565	203.3 Da LogP -0.54 TPSA 92.6	✓ Ro5	✓ Clean	`NCCCN(CCCN)CCC(=O)O`
ZINC79670384 ZINC	0.565	202.3 Da LogP -0.41 TPSA 106.4	✓ Ro5	✓ Clean	`CC(C)[C@@H](C(=O)[C@H](C)N)[C@H](N)C(=O)O`
ZINC79670387 ZINC	0.565	202.3 Da LogP -0.41 TPSA 106.4	✓ Ro5	✓ Clean	`CC(C)[C@H](C(=O)[C@H](C)N)[C@H](N)C(=O)O`
ZINC1605717 ZINC	0.552	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](C(=O)O)C(C)C`
ZINC1605718 ZINC	0.552	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@H](C(=O)O)C(C)C`
ZINC1605719 ZINC	0.552	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](C(=O)O)C(C)C`
ZINC1605720 ZINC	0.552	230.3 Da LogP 0.59 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@@H](C(=O)O)C(C)C`
ZINC13433578 ZINC	0.550	201.3 Da LogP 1.68 TPSA 80.4	✓ Ro5	✓ Clean	`NC(=O)CCCCCCCCC(=O)O`
ZINC201768036 ZINC	0.542	279.3 Da LogP -0.12 TPSA 100.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCCC(=O)O`
ZINC1616450 ZINC	0.536	254.3 Da LogP -1.28 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)[C@@H]1CCCN1)[C@@H]1CCCN1`
ZINC5600257 ZINC	0.536	254.3 Da LogP -1.28 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)[C@H]1CCCN1)[C@H]1CCCN1`
ZINC8655607 ZINC	0.536	254.3 Da LogP -1.28 TPSA 82.3	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)[C@H]1CCCN1)[C@@H]1CCCN1`
ZINC13529436 ZINC	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N1CCCCCC1`
ZINC1541834 ZINC	0.533	218.3 Da LogP -1.08 TPSA 112.7	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](CO)C(=O)O`
ZINC19502834 ZINC	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@@H](N)C(=O)N1CCCCCC1`
ZINC19502836 ZINC	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](N)C(=O)N1CCCCCC1`
ZINC19502838 ZINC	0.533	212.3 Da LogP 1.76 TPSA 46.3	✓ Ro5	✓ Clean	`CC[C@@H](C)[C@H](N)C(=O)N1CCCCCC1`
ZINC227596999 ZINC	0.533	357.5 Da LogP 1.51 TPSA 121.5	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](CC(C)C)C(=O)N[C@H](CC…`
ZINC227597004 ZINC	0.533	357.5 Da LogP 1.51 TPSA 121.5	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](CC(C)C)C(=O)N[C@H](C…`
ZINC2556618 ZINC	0.533	246.3 Da LogP -0.60 TPSA 129.7	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@@H](CC(=O)O)C(=O)O`
ZINC4556667 ZINC	0.533	357.5 Da LogP 1.51 TPSA 121.5	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](CC(C)C)C(=O)N[C@@H](C…`
ZINC4556684 ZINC	0.533	218.3 Da LogP -1.08 TPSA 112.7	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@@H](CO)C(=O)O`
ZINC4556685 ZINC	0.533	218.3 Da LogP -1.08 TPSA 112.7	✓ Ro5	✓ Clean	`CC(C)C[C@@H](N)C(=O)N[C@H](CO)C(=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.

Sequence

UniProt A0A0H3GZM8