KpKP13 Protein target profile

putative high-affinity branched-chain amino acid transporter periplasmic binding component

Accession: KP13_05285

Gene: AHE44692.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GT65

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Length 423

Pocket druggability (P2Rank · AlphaFold DB model) 0.192

Direct ligand evidence 0 55 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

Microbiome similarity 120 of 4744 screened genomes (2.5%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.34. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.19.

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): Y
DEG identity (%): 77.143 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 93.63 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) 0.192

Structure A0A0H3GT65

Pocket Pocket 1

Druggability (FPocket) 0.341

Structure A0A0H3GT65

Pocket Pocket 10

ColabFold model

P2Rank 0.087 · Pocket 1

FPocket 0.265 · Pocket 4

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.

MQRRTLLKAFALSASVMAMGLSFQAYAADTIKVGIMHSLSGTMAISETPLKDVALMAIDDINAKGGVLGKKLEPVVVDPASNWPLFAEKARQLLAQDKVAVVFGCWTSVSRKSVLPVFEELNGLLFYPVQYEGEEMSPNVFYTGAAPNQQAIPAVEYLLSEDGGGAKRFFLLGTDYVYPRTTNKILRAFLHAKGIQDKDIEEVYTPFGYSDYQTIVANIKKFAAGGKTAVVSTINGDSNVPFYKELANQGLKATDVPVVAFSVGEEELRGIDTKPLVGNLAAWNYFESVDNPTNKAFVADYRAYAKAHKLPNADTVVTNDPMEATWVGLHMWAQAVTKAGTTDVDKVREAMAGQTFNAPSGFTLTMDATNHHLHKPVMIGEIEGNGQFNVVWQTDKPVRAQPWSPWIPGNDKKPDHPVKTVSQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Subcellular localization

Localization: Unknown

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.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

24 records

Show feature table

Start	End	DB	Term	Name
5	16	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
290	303	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
290	303	InterPro	IPR000709	Leu/Ile/Val-binding protein
31	47	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
31	47	InterPro	IPR000709	Leu/Ile/Val-binding protein
53	69	PRINTS	PR00337	Leu/Ile/Val-binding protein family signature
53	69	InterPro	IPR000709	Leu/Ile/Val-binding protein
34	375	Gene3D	G3DSA:3.40.50.2300	-
28	423	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1	27	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
32	394	CDD	cd06355	PBP1_FmdD-like
32	394	InterPro	IPR017777	Urea ABC transporter, substrate-binding protein UrtA-like
146	390	Gene3D	G3DSA:3.40.50.2300	-
31	404	NCBIfam	TIGR03407	urea ABC transporter substrate-binding protein
31	404	InterPro	IPR017777	Urea ABC transporter, substrate-binding protein UrtA-like
30	409	SUPERFAMILY	SSF53822	Periplasmic binding protein-like I
30	409	InterPro	IPR028082	Periplasmic binding protein-like I
1	27	SignalP_EUK	SignalP-noTM	SignalP-noTM
401	423	MobiDBLite	mobidb-lite	consensus disorder prediction
31	407	Pfam	PF13433	Periplasmic binding protein domain
1	416	PANTHER	PTHR47628	-
1	4	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	27	Phobius	SIGNAL_PEPTIDE	Signal peptide region
17	27	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.

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

0.192

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Surrounding area

Pocket 2 P2Rank #2

0.021

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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 #10

0.341

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Surrounding area

Pocket 2 FPocket #9

0.22

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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

0.087

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Surrounding area

Pocket 2 P2Rank #2

0.015

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Surrounding area

Pocket 3 P2Rank #3

0.011

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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_A0A0H3GT65	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_05285	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.

55 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 5 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

ACM PDB via homolog 59.1 Da · LogP -0.51 · TPSA 43.1 Open detail RCSB PDB

BMD PDB via homolog Detail RCSB PDB

DHB PDB via homolog Detail RCSB PDB

PHB PDB via homolog Detail RCSB PDB

VNL PDB via homolog Detail RCSB PDB

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
ACM RCSB PDB	1PEA	P27017	59.1 Da LogP -0.51 TPSA 43.1	✓ Ro5	✓ Clean	`CC(=O)N`
BMD RCSB PDB	1QNL	P27017	87.1 Da LogP 0.27 TPSA 43.1	✓ Ro5	✓ Clean	`CCCC(=O)N`
DHB RCSB PDB	4EYK	Q13AR6	154.1 Da LogP 0.80 TPSA 77.8	✓ Ro5	Alert	`c1cc(c(cc1C(=O)O)O)O`
PHB RCSB PDB	4EY3	Q13AR6	138.1 Da LogP 1.09 TPSA 57.5	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)O)O`
VNL RCSB PDB	4EYG	Q13AR6	167.1 Da LogP -0.24 TPSA 69.6	✓ Ro5	✓ Clean	`COc1cc(ccc1O)C(=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
ZINC389804 ZINC	0.842	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(O)cc2)cc1`
ZINC1747299 ZINC	0.750	302.3 Da LogP 2.18 TPSA 93.1	✓ Ro5	Alert	`COc1cc(C(=O)C(=O)c2ccc(O)c(OC)c2)ccc1O`
ZINC33246180 ZINC	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccc(O)cc2)cc1`
ZINC3896282 ZINC	0.727	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccc(O)cc2)cc1`
ZINC392302 ZINC	0.727	230.2 Da LogP 2.88 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(O)cc2)cc1`
ZINC289893 ZINC	0.696	278.3 Da LogP 1.92 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(S(=O)(=O)c2ccc(O)cc2)cc1`
ZINC1595860 ZINC	0.677	316.3 Da LogP 2.48 TPSA 82.1	✓ Ro5	Alert	`COc1cc(C(=O)C(=O)c2ccc(OC)c(OC)c2)ccc1O`
ZINC114185151 ZINC	0.667	298.2 Da LogP 2.15 TPSA 108.7	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC2924369 ZINC	0.667	242.2 Da LogP 2.16 TPSA 74.6	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccc(O)cc1`
ZINC103291148 ZINC	0.656	356.4 Da LogP 3.52 TPSA 93.1	✓ Ro5	✓ Clean	`COc1cc(C(=O)/C(C)=C(/C)C(=O)c2ccc(O)c(OC)c2)ccc…`
ZINC3156317 ZINC	0.640	258.2 Da LogP 2.31 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(=O)c2ccc(O)cc2)cc1`
ZINC4903179 ZINC	0.640	257.2 Da LogP 2.34 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2ccc(O)cc2)cc1`
ZINC134079 ZINC	0.632	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1640789 ZINC	0.632	374.3 Da LogP 3.55 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)c3ccc(C(=O)O)cc3)cc…`
ZINC1693895 ZINC	0.632	227.4 Da LogP 4.17 TPSA 43.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCC(N)=O`
ZINC2146859 ZINC	0.632	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC2170606 ZINC	0.632	213.4 Da LogP 3.78 TPSA 43.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCC(N)=O`
ZINC28449 ZINC	0.632	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(O)cc1`
ZINC3147211 ZINC	0.632	318.3 Da LogP 4.42 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC332365 ZINC	0.632	318.3 Da LogP 3.56 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(c1ccc(O)cc1)c1ccc(C(=O)c2ccc(O)cc2)cc1`
ZINC86040350 ZINC	0.632	241.4 Da LogP 4.56 TPSA 43.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCC(N)=O`
ZINC8689949 ZINC	0.632	255.4 Da LogP 4.95 TPSA 43.1	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCCCC(N)=O`
ZINC1705144 ZINC	0.619	226.2 Da LogP 2.46 TPSA 54.4	✓ Ro5	Alert	`O=C(C(=O)c1ccc(O)cc1)c1ccccc1`
ZINC1747330 ZINC	0.618	362.3 Da LogP 2.13 TPSA 111.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)OCCOC(=O)c2ccc(O)c(OC)c2)ccc1O`
ZINC38237511 ZINC	0.618	242.3 Da LogP 2.94 TPSA 46.5	✓ Ro5	✓ Clean	`COc1cc(C(=O)c2ccc(C)cc2)ccc1O`
ZINC262158 ZINC	0.615	214.2 Da LogP 2.33 TPSA 57.5	✓ Ro5	Alert	`O=C(c1ccccc1)c1ccc(O)c(O)c1`
ZINC2384798 ZINC	0.607	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@@H](C)C(=O)O`
ZINC49181262 ZINC	0.600	372.4 Da LogP 2.73 TPSA 105.6	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@@]2(C)O[C@@]2(C)C(=O)c2ccc(O)c(O…`
ZINC49181265 ZINC	0.600	372.4 Da LogP 2.73 TPSA 105.6	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@@]2(C)O[C@]2(C)C(=O)c2ccc(O)c(OC…`
ZINC49181268 ZINC	0.600	372.4 Da LogP 2.73 TPSA 105.6	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@]2(C)O[C@@]2(C)C(=O)c2ccc(O)c(OC…`
ZINC6338454 ZINC	0.593	268.3 Da LogP 2.99 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/C(=O)c2ccc(O)cc2)cc1`
ZINC2391059 ZINC	0.586	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@H](C(=O)O)[C@@H](C)CC`
ZINC40472549 ZINC	0.586	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](N)C(=O)N[C@@H](C(=O)O)[C@@H](C)…`
ZINC40490721 ZINC	0.586	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@@H](NC(=O)[C@@H](N)[C@H](C)CC)C(=O…`
ZINC5909388 ZINC	0.586	244.3 Da LogP 0.98 TPSA 92.4	✓ Ro5	✓ Clean	`CC[C@H](C)[C@H](NC(=O)[C@@H](N)[C@H](C)CC)C(=O)O`
ZINC1747304 ZINC	0.583	288.3 Da LogP 2.54 TPSA 76.0	✓ Ro5	✓ Clean	`COc1cc(CC(=O)c2ccc(O)c(OC)c2)ccc1O`
ZINC266 ZINC	0.583	223.3 Da LogP 1.88 TPSA 49.8	✓ Ro5	✓ Clean	`CCN(CC)C(=O)c1ccc(O)c(OC)c1`
ZINC36108805 ZINC	0.583	224.2 Da LogP 1.45 TPSA 83.8	✓ Ro5	✓ Clean	`COc1cc(C(=O)CCC(=O)O)ccc1O`
ZINC65340137 ZINC	0.583	258.2 Da LogP 2.46 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)cc(-c2ccc(O)cc2)c1`
ZINC167246 ZINC	0.571	248.0 Da LogP 1.99 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)cc1`
ZINC3269660 ZINC	0.571	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC34573580 ZINC	0.571	496.5 Da LogP 4.86 TPSA 149.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(c2ccc(C(=O)O)cc2)(c2ccc(C(=O)O)cc…`
ZINC388063 ZINC	0.571	201.0 Da LogP 2.15 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Br)cc1`
ZINC13340359 ZINC	0.568	212.2 Da LogP -0.06 TPSA 87.0	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@H](O)CO)ccc1O`
ZINC13340360 ZINC	0.568	212.2 Da LogP -0.06 TPSA 87.0	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@@H](O)CO)ccc1O`
ZINC1668317 ZINC	0.568	210.2 Da LogP 1.97 TPSA 55.8	✓ Ro5	✓ Clean	`CCCOC(=O)c1ccc(O)c(OC)c1`
ZINC1747307 ZINC	0.568	304.3 Da LogP 2.03 TPSA 96.2	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@H](O)c2ccc(O)c(OC)c2)ccc1O`
ZINC2042188 ZINC	0.568	304.3 Da LogP 2.03 TPSA 96.2	✓ Ro5	✓ Clean	`COc1cc(C(=O)[C@@H](O)c2ccc(O)c(OC)c2)ccc1O`
ZINC75616154 ZINC	0.568	208.3 Da LogP 2.77 TPSA 46.5	✓ Ro5	✓ Clean	`CCCCC(=O)c1ccc(O)c(OC)c1`
ZINC82722760 ZINC	0.568	238.2 Da LogP 1.54 TPSA 72.8	✓ Ro5	✓ Clean	`COC(=O)CCC(=O)c1ccc(O)c(OC)c1`

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 A0A0H3GT65