Protein target profile

KP13_02266

Transcriptional activator protein lysR

Genome: KpKP13 Gene: lysR AHE42839.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GXX4

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Length 308

Pocket druggability 0.041

Direct ligand evidence 0 56 total records

Functional annotation 0 EC 5 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.

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: 2.3% 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: 92.04 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 0.041

Structure A0A0H3GXX4

Pocket Pocket 12

P2Rank 0.77

Structure A0A0H3GXX4

Pocket Pocket 1

ColabFold model

FPocket 0.285 · Pocket 16

P2Rank 0.694 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 110 / 4744 genomes with a hit

Prevalence 2.3%

Cross-references

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

Sequence

UniProt A0A0H3GXX4

Sequence

Primary amino-acid sequence viewer.

MPAVNLRHIEIFHAVMTTGNLTEAARMLHTSQPTVSRELARFEKVLGLQLFERTRGRLQPTVQGLRLFEEVQRSWYGLDRIVSAAESLREFRQGELSIACLPVFSQSFLPLLLPPFLARYPEVSLQIVPQESPLLEEWLSAQRHDLGLTETLHTPAGTERTPLLTLNEVCVLPAGHPLAAQATLTPADFQGENYISLSRTDSYRQLLDALFLEHQVKRRMVVETHSAASICAMVRAGAGISVVNPLTALDYADSGVVVRRFSVEVPFTVSLIRPLHRPRSALVDAFVAHLQQSLPQILTPLASVLQRA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

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.
GO:0043565 Binding to DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
GO:0009089 OBSOLETE. The chemical reactions and pathways resulting in the formation of lysine, via the intermediate diaminopimelate.
GO:0010628 Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product (protein or RNA).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
93	298	SUPERFAMILY	SSF53850	Periplasmic binding protein-like II
96	297	Gene3D	G3DSA:3.40.190.290	-
3	84	SUPERFAMILY	SSF46785	Winged helix DNA-binding domain
3	84	InterPro	IPR036390	Winged helix DNA-binding domain superfamily
1	303	PANTHER	PTHR30427	TRANSCRIPTIONAL ACTIVATOR PROTEIN LYSR
92	294	Pfam	PF03466	LysR substrate binding domain
92	294	InterPro	IPR005119	LysR, substrate-binding
3	87	FunFam	G3DSA:1.10.10.10:FF:000174	LysR family transcriptional regulator
1	86	Gene3D	G3DSA:1.10.10.10	-
1	86	InterPro	IPR036388	Winged helix-like DNA-binding domain superfamily
6	64	Pfam	PF00126	Bacterial regulatory helix-turn-helix protein, lysR family
6	64	InterPro	IPR000847	Transcription regulator HTH, LysR
4	61	ProSiteProfiles	PS50931	LysR-type HTH domain profile.
4	61	InterPro	IPR000847	Transcription regulator HTH, LysR
32	42	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
32	42	InterPro	IPR000847	Transcription regulator HTH, LysR
42	53	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
42	53	InterPro	IPR000847	Transcription regulator HTH, LysR
21	32	PRINTS	PR00039	LysR bacterial regulatory protein HTH signature
21	32	InterPro	IPR000847	Transcription regulator HTH, LysR
96	297	FunFam	G3DSA:3.40.190.290:FF:000007	LysR family transcriptional regulator

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

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

Site 1 P2Rank #1

0.77

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Surrounding area

Site 2 P2Rank #2

0.006

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Surrounding area

Site 3 P2Rank #3

0.004

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Surrounding area

Site 4 P2Rank #4

0.003

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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_A0A0H3GXX4	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_02266	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.

56 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 6 records from similar proteins

Structural ligands 6 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

6DB PDB via homolog 246.3 Da · LogP -1.23 · TPSA 148.5 Open detail RCSB PDB

AKG PDB via homolog Detail RCSB PDB

OAS PDB via homolog Detail RCSB PDB

RUB PDB via homolog Detail RCSB PDB

SAC 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
6DB RCSB PDB	5VVI	P0A4T4	246.3 Da LogP -1.23 TPSA 148.5	1 viol.	✓ Clean	`[H]/N=C(/N)\NCCC[C@@H](C(=O)O)N[C@H](C)C(=O)O`
AKG RCSB PDB	5Y2V	P73862	146.1 Da LogP -0.50 TPSA 91.7	✓ Ro5	✓ Clean	`C(CC(=O)O)C(=O)C(=O)O`
OAS RCSB PDB	4LQ2	P06614	147.1 Da LogP -1.04 TPSA 89.6	✓ Ro5	✓ Clean	`CC(=O)OC[C@@H](C(=O)O)N`
RUB RCSB PDB	5Z49	Q9F1R2	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`C([C@H]([C@H](C(=O)COP(=O)(O)O)O)O)OP(=O)(O)O`
SAC RCSB PDB	4M4G	P06614	147.1 Da LogP -1.43 TPSA 86.6	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CO)C(=O)O`
SKM RCSB PDB	5TED	Q8Y9N7	174.2 Da LogP -1.52 TPSA 98.0	✓ Ro5	✓ Clean	`C1[C@H]([C@@H]([C@@H](C=C1C(=O)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
ZINC3870277 ZINC	1.000	310.1 Da LogP -2.50 TPSA 191.0	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1529866 ZINC	0.833	246.3 Da LogP -1.23 TPSA 148.5	1 viol.	✓ Clean	`C[C@H](N[C@@H](CCCNC(=N)N)C(=O)O)C(=O)O`
ZINC1529867 ZINC	0.833	246.3 Da LogP -1.23 TPSA 148.5	1 viol.	✓ Clean	`C[C@@H](N[C@@H](CCCNC(=N)N)C(=O)O)C(=O)O`
ZINC12502210 ZINC	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@@H](O)COP(=O…`
ZINC12502212 ZINC	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)[C@H](O)COP(=O)…`
ZINC12502214 ZINC	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@@H](O)COP(=…`
ZINC12502216 ZINC	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)[C@H](O)COP(=O…`
ZINC4523251 ZINC	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@@H](O)COP(…`
ZINC4523255 ZINC	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)[C@H](O)COP(=…`
ZINC4523257 ZINC	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@@H](O)COP(=…`
ZINC4523259 ZINC	0.793	340.1 Da LogP -3.14 TPSA 211.3	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)COP(=O…`
ZINC1529626 ZINC	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC1532567 ZINC	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1532851 ZINC	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC30320708 ZINC	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC31259596 ZINC	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)CO`
ZINC31259600 ZINC	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@@H](O)CO`
ZINC3869804 ZINC	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@@H](O)CO`
ZINC3869805 ZINC	0.724	230.1 Da LogP -2.62 TPSA 144.5	✓ Ro5	✓ Clean	`O=C(COP(=O)(O)O)[C@H](O)[C@H](O)CO`
ZINC1560408815 ZINC	0.656	339.1 Da LogP -1.87 TPSA 214.1	1 viol.	✓ Clean	`[O]/C(COP(=O)(O)O)=C(/O)[C@H](O)[C@H](O)COP(=O)…`
ZINC5830339 ZINC	0.645	231.1 Da LogP -2.68 TPSA 156.5	1 viol.	✓ Clean	`O=C(NO)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC18140538 ZINC	0.625	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(COP(=O)(O)O)[C@@H](O)[C@H](O)[C@H](O)CO`
ZINC100029384 ZINC	0.594	244.1 Da LogP -2.23 TPSA 144.5	✓ Ro5	✓ Clean	`C[C@H](O)[C@@H](O)[C@@H](O)C(=O)COP(=O)(O)O`
ZINC1602740 ZINC	0.593	201.2 Da LogP 0.19 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](C[C@H](C)C(C)=O)C(=O)O`
ZINC1602741 ZINC	0.593	201.2 Da LogP 0.19 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](C[C@@H](C)C(C)=O)C(=O)O`
ZINC1602742 ZINC	0.593	201.2 Da LogP 0.19 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@H](C[C@H](C)C(C)=O)C(=O)O`
ZINC1602743 ZINC	0.593	201.2 Da LogP 0.19 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@H](C[C@@H](C)C(C)=O)C(=O)O`
ZINC2560841 ZINC	0.586	204.2 Da LogP -2.32 TPSA 115.7	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CO)C(=O)NCC(=O)O`
ZINC1706207 ZINC	0.583	202.2 Da LogP 0.32 TPSA 69.7	✓ Ro5	✓ Clean	`CC(=O)OCC(COC(C)=O)C(C)=O`
ZINC100065511 ZINC	0.576	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@@H](O)COP(=O)(O)O`
ZINC100085043 ZINC	0.576	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC104869937 ZINC	0.576	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@@H](O)COP(=O)(O)O`
ZINC13537943 ZINC	0.576	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@H](O)[C@@H](O)[C@H](O)COP(=O)(O)O`
ZINC85994845 ZINC	0.576	260.1 Da LogP -3.26 TPSA 164.8	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)COP(=O)(O)O`
ZINC1529261 ZINC	0.571	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`N=C(N)NCCC[C@@H](N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC1529262 ZINC	0.571	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`N=C(N)NCCC[C@@H](N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC1529939 ZINC	0.571	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC1529940 ZINC	0.571	304.3 Da LogP -1.39 TPSA 185.8	1 viol.	✓ Clean	`N=C(N)NCCC[C@H](N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC2019971 ZINC	0.571	205.2 Da LogP -0.14 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSC(C)=O)C(=O)O`
ZINC6186192 ZINC	0.571	205.2 Da LogP -0.14 TPSA 83.5	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CSC(C)=O)C(=O)O`
ZINC2539634 ZINC	0.567	207.3 Da LogP -0.70 TPSA 86.6	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSCCO)C(=O)O`
ZINC70665010 ZINC	0.567	287.4 Da LogP 3.73 TPSA 72.5	✓ Ro5	✓ Clean	`CCCCCCCCCCCCCOC[C@@H](N)C(=O)O`
ZINC71773060 ZINC	0.567	207.2 Da LogP 0.37 TPSA 66.4	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CO)C(=O)c1ccccc1`
ZINC71773061 ZINC	0.567	207.2 Da LogP 0.37 TPSA 66.4	✓ Ro5	✓ Clean	`CC(=O)N[C@H](CO)C(=O)c1ccccc1`
ZINC2522560 ZINC	0.564	204.2 Da LogP -0.76 TPSA 112.6	✓ Ro5	✓ Clean	`C[C@@H](N[C@@H](CCCN)C(=O)O)C(=O)O`
ZINC22067319 ZINC	0.563	267.3 Da LogP -1.98 TPSA 127.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSC[C@@H](O)[C@@H](O)CO)C(=O)O`
ZINC22067322 ZINC	0.563	267.3 Da LogP -1.98 TPSA 127.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSC[C@H](O)[C@@H](O)CO)C(=O)O`
ZINC22067325 ZINC	0.563	267.3 Da LogP -1.98 TPSA 127.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSC[C@@H](O)[C@H](O)CO)C(=O)O`
ZINC22067328 ZINC	0.563	267.3 Da LogP -1.98 TPSA 127.1	✓ Ro5	✓ Clean	`CC(=O)N[C@@H](CSC[C@H](O)[C@H](O)CO)C(=O)O`
ZINC5132038 ZINC	0.559	290.2 Da LogP -3.90 TPSA 185.0	1 viol.	✓ Clean	`O=C(CO)[C@@H](O)[C@H](O)[C@H](O)[C@H](O)COP(=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.

KP13_02266

Promising target candidate with multiple supporting evidence streams.

Main supporting evidence

Risks to review

Evidence gaps

Prioritization evidence

Off-target risk

Essentiality

Localization

Structure confidence

Binding-site evidence

Cross-references

Sequence

Sequence

Functional annotations

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · P2Rank

Binding pockets · FPocket

Binding pockets · P2Rank

Structural evidence

Ligand evidence