Protein target profile

KP13_02480

HTH-type transcriptional regulator

Genome: KpKP13 Gene: AHE46492.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GM46

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Length 287

Pocket druggability 0.856

Direct ligand evidence 0 53 total records

Functional annotation 0 EC 4 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

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.86. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + 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: 0.5% 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.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 93.42 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 0.856

Structure A0A0H3GM46

Pocket Pocket 2

P2Rank 0.092

Structure A0A0H3GM46

Pocket Pocket 1

ColabFold model

FPocket 0.668 · Pocket 6

P2Rank 0.079 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 23 / 4744 genomes with a hit

Prevalence 0.5%

Cross-references

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

Sequence

UniProt A0A0H3GM46

Sequence

Primary amino-acid sequence viewer.

MSWSIDIISCITDRFVELTATEKRIAQFILDDVATAAELPIAEIARLTQTSQASVTRFARALGCKDVRELKMKLAQSLAVGQRFILDVPDLEGVQGIYESIISVLETNRRALDIEALKRAVSWLSDARQILALGMGGGSTICAQEIQYRLFRLGLPVVSQSDGLLVRMMSSAVTPQDVVIVLSLGGYTREIIESAAIASQYGAKVIAISPAGTPLAEQADLVLPLLVRENDYIFKPSTSRYAMLAMVDVLATELAMANKTQAKGKLRRIKLALDSHRGGVDRQPLGD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

GO:1901135 The chemical reactions and pathways involving carbohydrate derivative.
GO:0097367 Binding to a carbohydrate derivative.
GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records

Show feature table

Start	End	DB	Term	Name
7	277	PANTHER	PTHR30514	GLUCOKINASE
7	277	InterPro	IPR047640	HTH-type transcriptional regulator RpiR-like
115	253	CDD	cd05013	SIS_RpiR
115	253	InterPro	IPR035472	RpiR-like, SIS domain
4	79	Gene3D	G3DSA:1.10.10.10	-
4	79	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
120	260	ProSiteProfiles	PS51464	SIS domain profile.
120	260	InterPro	IPR001347	SIS domain
10	79	Pfam	PF01418	Helix-turn-helix domain, rpiR family
10	79	InterPro	IPR000281	Helix-turn-helix protein RpiR
95	259	SUPERFAMILY	SSF53697	SIS domain
95	259	InterPro	IPR046348	SIS domain superfamily
5	81	ProSiteProfiles	PS51071	RpiR-type HTH domain profile.
5	81	InterPro	IPR000281	Helix-turn-helix protein RpiR
124	252	Pfam	PF01380	SIS domain
124	252	InterPro	IPR001347	SIS domain
94	273	Gene3D	G3DSA:3.40.50.10490	-
5	79	SUPERFAMILY	SSF46689	Homeodomain-like
5	79	InterPro	IPR009057	Homeobox-like domain superfamily

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 #2

0.856

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Surrounding area

Site 2 FPocket #6

0.379

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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.092

Show in viewer

Surrounding area

Site 2 P2Rank #2

0.005

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_A0A0H3GM46	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_02480	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

4QY PDB via homolog 301.2 Da · LogP -2.96 · TPSA 165.8 Open detail RCSB PDB

J79 PDB via homolog Detail RCSB PDB

MXE PDB via homolog Detail RCSB PDB

ZINC100350901 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC1530414 ZINC proposed compound · Tanimoto 1.000 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
4QY RCSB PDB	7EN5	P77245	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H]([C@@H]([C@H](O[C@H]1O)COP(=…`
J79 RCSB PDB	7EN7	P77245	373.3 Da LogP -2.46 TPSA 192.1	1 viol.	✓ Clean	`C[C@H](C(=O)O)O[C@@H]1[C@H]([C@@H](O[C@@H]([C@H…`
MXE RCSB PDB	3IWF	A0A0H2VHQ2	76.1 Da LogP -0.37 TPSA 29.5	✓ Ro5	✓ Clean	`COCCO`

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
ZINC100350901 ZINC	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](COP(=O)(O)O)[C@H](…`
ZINC1530414 ZINC	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)O[C@@H](COP(=O)(O)O)[C@H…`
ZINC1532625 ZINC	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@H](O)[C@@H](O)[C@H](COP(=O)(O)O…`
ZINC245204467 ZINC	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@H](O)[C@@H](O)[C@@H](COP(=O)(O)…`
ZINC245204468 ZINC	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@H](O)[C@H](O)[C@@H](COP(=O)(O)O…`
ZINC30725207 ZINC	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](COP(=O)(O)O)[C@@H]…`
ZINC4096363 ZINC	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)O[C@H](COP(=O)(O)O)[C@@H…`
ZINC4097100 ZINC	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](COP(=O)(O)O)[C@@H]…`
ZINC4097101 ZINC	1.000	301.2 Da LogP -2.96 TPSA 165.8	1 viol.	✓ Clean	`CC(=O)N[C@H]1[C@H](O)O[C@H](COP(=O)(O)O)[C@@H](…`
ZINC3861769 ZINC	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC4096938 ZINC	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC4245657 ZINC	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@@H…`
ZINC44608202 ZINC	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@H](O)[C@@H]1…`
ZINC62227779 ZINC	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O[C@@H](C)C(=O)O)[C@@H](O)[C…`
ZINC71755829 ZINC	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H…`
ZINC71755842 ZINC	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@@…`
ZINC79670001 ZINC	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@@H…`
ZINC8585107 ZINC	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1…`
ZINC8585110 ZINC	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1…`
ZINC8602542 ZINC	0.708	293.3 Da LogP -2.58 TPSA 145.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O[C@H](C)C(=O)O)[C@@H](O)[C@…`
ZINC1580161 ZINC	0.647	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118 ZINC	0.647	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257 ZINC	0.647	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654 ZINC	0.647	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC44076059 ZINC	0.647	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101 ZINC	0.647	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5997860 ZINC	0.647	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC13543977 ZINC	0.628	301.3 Da LogP -3.25 TPSA 162.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](COS(=O)(=O)O)[C@H]…`
ZINC13543979 ZINC	0.628	301.3 Da LogP -3.25 TPSA 162.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](COS(=O)(=O)O)[C@@H…`
ZINC4096329 ZINC	0.628	301.3 Da LogP -3.25 TPSA 162.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)O[C@H](COS(=O)(=O)O)[C@@H]…`
ZINC4096360 ZINC	0.628	301.3 Da LogP -3.25 TPSA 162.6	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)O[C@H](COS(=O)(=O)O)[C@H](…`
ZINC12504154 ZINC	0.622	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@@H](O)[C@@H]1O`
ZINC1532546 ZINC	0.622	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@@H]1O[C@H](O)[C@@H](O)[C@H]1O`
ZINC4096190 ZINC	0.622	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@H](O)[C@H](O)[C@@H]1O`
ZINC4228241 ZINC	0.622	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@H](O)[C@@H]1O`
ZINC4521831 ZINC	0.622	230.1 Da LogP -2.47 TPSA 136.7	✓ Ro5	✓ Clean	`O=P(O)(O)OC[C@H]1O[C@@H](O)[C@@H](O)[C@@H]1O`
ZINC1042045 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)[C@H](O)[C@H](CO)O[C@H]1O`
ZINC16124914 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC2562219 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@H](O)[C@@H]1O`
ZINC3860151 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC3870075 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@@H](O)[C@H]…`
ZINC3983907 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]1O`
ZINC4228290 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)O[C@H](CO)[C@@H](O)[C@@H]…`
ZINC4293686 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)[C@@H](O)[C@@H](CO)O[C@H]1O`
ZINC4301186 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@@H](O)O[C@H](CO)[C@H](O)[C@@H]…`
ZINC5227360 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)[C@H](O)[C@@H](CO)O[C@H]1O`
ZINC5883957 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)[C@H](O)[C@@H](CO)O[C@H]1O`
ZINC5883978 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@H](O)O[C@@H](CO)[C@H](O)[C@@H]1O`
ZINC895332 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@H]1[C@@H](O)O[C@@H](CO)[C@H](O)[C@H]1O`
ZINC901459 ZINC	0.615	221.2 Da LogP -3.08 TPSA 119.3	✓ Ro5	✓ Clean	`CC(=O)N[C@@H]1[C@H](O)[C@@H](O)[C@@H](CO)O[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.