Protein target profile

KP13_00486

Divalent-cation tolerance protein cutA

Genome: KpKP13 Gene: AHE46779.1 cutA 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GH55

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Length 108

Pocket druggability 0.035

Direct ligand evidence 0 52 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.

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: Hit
Human identity (%): 40.541 Lower values reduce human off-target concern.
Human E-value: 8.45e-16
Gut microbiome similarity: 2.0% 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: 96.33 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 0.035

Structure A0A0H3GH55

Pocket Pocket 1

P2Rank 0.123

Structure A0A0H3GH55

Pocket Pocket 1

ColabFold model

FPocket 0.168 · Pocket 1

P2Rank 0.114 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 95 / 4744 genomes with a hit

Prevalence 2.0%

Cross-references

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

Sequence

UniProt A0A0H3GH55

Sequence

Primary amino-acid sequence viewer.

MMTTPDAVVVLCTAPDEATAQDLAAKALAEKVAACATLLPGATSLYYWEGKLEQEYEVQMLLKTDLAHQQALLDCLKSHHPYQTPELLVLPVTHGDNDYLSWLTASLR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0005507 Binding to a copper (Cu) ion.
GO:0010038 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a metal ion stimulus.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
1	6	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
1	20	Phobius	SIGNAL_PEPTIDE	Signal peptide region
2	108	Hamap	MF_01160	Divalent-cation tolerance protein CutA [cutA].
2	108	InterPro	IPR023700	Divalent cation tolerance protein CutA, Enterobacteria
7	14	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
4	107	SUPERFAMILY	SSF54913	GlnB-like
4	107	InterPro	IPR011322	Nitrogen regulatory PII-like, alpha/beta
21	108	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
8	105	Pfam	PF03091	CutA1 divalent ion tolerance protein
8	105	InterPro	IPR004323	Divalent ion tolerance protein, CutA
6	107	PANTHER	PTHR23419	DIVALENT CATION TOLERANCE CUTA-RELATED
6	107	InterPro	IPR004323	Divalent ion tolerance protein, CutA
15	20	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
1	108	Gene3D	G3DSA:3.30.70.120	-
1	108	InterPro	IPR015867	Nitrogen regulatory protein PII/ATP phosphoribosyltransferase, C-terminal
1	108	FunFam	G3DSA:3.30.70.120:FF:000004	Divalent-cation tolerance protein CutA

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

0.123

Show in viewer

Surrounding area

Residue sets

UniProt: Binding site:11-11

UniProt: Binding site:78-78

UniProt: Binding site:79-79

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_A0A0H3GH55	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_00486	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.

52 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 2 records from similar proteins

Structural ligands 2 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

BTB PDB via homolog 209.2 Da · LogP -3.01 · TPSA 104.4 Open detail RCSB PDB

MBO PDB via homolog Detail RCSB PDB

ZINC1615342 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC114185151 ZINC proposed compound · Tanimoto 0.632 Detail ZINC

ZINC134079 ZINC proposed compound · Tanimoto 0.600 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
BTB RCSB PDB	6GDV	Q31KX8	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`C(CO)N(CCO)C(CO)(CO)CO`
MBO RCSB PDB	1NAQ	P69488	321.7 Da LogP 0.56 TPSA 37.3	✓ Ro5	✓ Clean	`c1cc(ccc1C(=O)O)[Hg]`

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
ZINC1615342 ZINC	1.000	209.2 Da LogP -3.01 TPSA 104.4	✓ Ro5	✓ Clean	`OCCN(CCO)C(CO)(CO)CO`
ZINC114185151 ZINC	0.632	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`
ZINC134079 ZINC	0.600	242.2 Da LogP 2.75 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(C(=O)O)cc2)cc1`
ZINC1640789 ZINC	0.600	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…`
ZINC2146859 ZINC	0.600	270.2 Da LogP 2.31 TPSA 91.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC3147211 ZINC	0.600	318.3 Da LogP 4.42 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC188555 ZINC	0.591	350.3 Da LogP 4.67 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(Oc3ccc(C(=O)O)cc3)cc2)cc1`
ZINC241160 ZINC	0.591	258.2 Da LogP 2.88 TPSA 83.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(C(=O)O)cc2)cc1`
ZINC389804 ZINC	0.565	214.2 Da LogP 2.76 TPSA 57.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(O)cc2)cc1`
ZINC392302 ZINC	0.560	230.2 Da LogP 2.88 TPSA 66.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(O)cc2)cc1`
ZINC167246 ZINC	0.545	248.0 Da LogP 1.99 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)cc1`
ZINC3269660 ZINC	0.545	254.2 Da LogP 2.45 TPSA 71.4	✓ Ro5	Alert	`O=C(O)c1ccc(C(=O)C(=O)c2ccccc2)cc1`
ZINC34573580 ZINC	0.545	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	0.545	201.0 Da LogP 2.15 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Br)cc1`
ZINC13375284 ZINC	0.522	270.2 Da LogP 3.50 TPSA 99.3	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccc(C(=O)O)cc2)cc1`
ZINC156520 ZINC	0.522	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C/c2ccc(C(=O)O)cc2)cc1`
ZINC1651850 ZINC	0.522	270.3 Da LogP 2.87 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(CCc2ccc(C(=O)O)cc2)cc1`
ZINC1759946 ZINC	0.522	256.3 Da LogP 2.67 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Cc2ccc(C(=O)O)cc2)cc1`
ZINC1857524265 ZINC	0.522	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C=Cc2ccc(C(=O)O)cc2)cc1`
ZINC2334905 ZINC	0.522	261.4 Da LogP 1.10 TPSA 63.9	✓ Ro5	✓ Clean	`CC(C)CCN(CCC(C)C)C(CO)(CO)CO`
ZINC2504355 ZINC	0.522	226.2 Da LogP 2.62 TPSA 54.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)c2ccccc2)cc1`
ZINC3159953 ZINC	0.522	261.4 Da LogP 1.38 TPSA 63.9	✓ Ro5	✓ Clean	`CCCCCN(CCCCC)C(CO)(CO)CO`
ZINC32299177 ZINC	0.522	266.3 Da LogP 2.48 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C#Cc2ccc(C(=O)O)cc2)cc1`
ZINC34009333 ZINC	0.522	376.4 Da LogP 3.96 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(c2ccc(C(=O)O)cc2)c2ccc(C(=O)O)cc2…`
ZINC34057267 ZINC	0.522	274.3 Da LogP 4.72 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2ccc(-c3ccccc3)cc2)cc1`
ZINC346855 ZINC	0.522	274.3 Da LogP 3.23 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Sc2ccc(C(=O)O)cc2)cc1`
ZINC4309722 ZINC	0.522	270.2 Da LogP 3.50 TPSA 99.3	✓ Ro5	Alert	`O=C(O)c1ccc(/N=N/c2ccc(C(=O)O)cc2)cc1`
ZINC4792283 ZINC	0.522	268.3 Da LogP 3.25 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(/C=C\c2ccc(C(=O)O)cc2)cc1`
ZINC59301968 ZINC	0.522	394.3 Da LogP 2.54 TPSA 111.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc(P(c2ccc(C(=O)O)cc2)c2ccc(C(=O)O)cc2…`
ZINC8418684 ZINC	0.522	257.2 Da LogP 2.83 TPSA 86.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Nc2ccc(C(=O)O)cc2)cc1`
ZINC95080304 ZINC	0.522	377.4 Da LogP 4.25 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(N(c2ccc(C(=O)O)cc2)c2ccc(C(=O)O)cc2…`
ZINC96024941 ZINC	0.522	366.4 Da LogP 3.88 TPSA 74.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C#Cc2ccc(C#Cc3ccc(C(=O)O)cc3)cc2)cc1`
ZINC112963478 ZINC	0.520	358.3 Da LogP 2.10 TPSA 127.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(=O)OCCOC(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC2163682 ZINC	0.520	302.3 Da LogP 2.54 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OCCOc2ccc(C(=O)O)cc2)cc1`
ZINC263618653 ZINC	0.520	302.2 Da LogP 2.82 TPSA 117.8	✓ Ro5	Alert	`O=C(O)c1ccc(O/N=N/Oc2ccc(C(=O)O)cc2)cc1`
ZINC3150492 ZINC	0.520	406.3 Da LogP 3.52 TPSA 127.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OC(=O)c2ccc(C(=O)Oc3ccc(C(=O)O)cc3)…`
ZINC60939 ZINC	0.520	214.2 Da LogP 3.18 TPSA 46.5	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccccc2)cc1`
ZINC642881183 ZINC	0.520	350.3 Da LogP 3.83 TPSA 115.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2cc(O)c(-c3ccc(C(=O)O)cc3)cc2O)cc1`
ZINC754399 ZINC	0.520	362.3 Da LogP 4.11 TPSA 100.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc(Oc2ccc(C(=O)c3ccc(C(=O)O)cc3)cc2)cc1`
ZINC1594026 ZINC	0.500	284.3 Da LogP 3.41 TPSA 74.6	✓ Ro5	✓ Clean	`CC(C)(c1ccc(C(=O)O)cc1)c1ccc(C(=O)O)cc1`
ZINC166414480 ZINC	0.500	322.3 Da LogP 2.00 TPSA 126.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2nnc(-c3ccc(C(=O)O)cc3)nn2)cc1`
ZINC1728705 ZINC	0.500	239.5 Da LogP 3.21 TPSA 37.3	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(Cl)(Cl)Cl)cc1`
ZINC1846432 ZINC	0.500	316.3 Da LogP 2.93 TPSA 93.1	✓ Ro5	✓ Clean	`O=C(O)c1ccc(OCCCOc2ccc(C(=O)O)cc2)cc1`
ZINC195408276 ZINC	0.500	300.4 Da LogP 1.91 TPSA 74.6	✓ Ro5	✓ Clean	`C[Si](C)(c1ccc(C(=O)O)cc1)c1ccc(C(=O)O)cc1`
ZINC2528579 ZINC	0.500	441.4 Da LogP 3.97 TPSA 150.6	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2nc(-c3ccc(C(=O)O)cc3)nc(-c3ccc(C…`
ZINC3129995 ZINC	0.500	446.5 Da LogP 2.75 TPSA 142.9	✓ Ro5	✓ Clean	`O=C(O)c1ccc(S(=O)(=O)c2ccc(S(=O)(=O)c3ccc(C(=O)…`
ZINC32189977 ZINC	0.500	272.3 Da LogP 2.16 TPSA 94.8	✓ Ro5	✓ Clean	`O=C(O)c1ccc(C(O)c2ccc(C(=O)O)cc2)cc1`
ZINC33246180 ZINC	0.500	242.2 Da LogP 3.51 TPSA 82.2	✓ Ro5	Alert	`O=C(O)c1ccc(N=Nc2ccc(O)cc2)cc1`
ZINC348142 ZINC	0.500	306.3 Da LogP 1.92 TPSA 108.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(S(=O)(=O)c2ccc(C(=O)O)cc2)cc1`
ZINC5580842 ZINC	0.500	316.3 Da LogP 2.89 TPSA 98.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=S)Nc2ccc(C(=O)O)cc2)cc1`

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_00486

Target candidate with partial support; inspect missing evidence before prioritizing.

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 · P2Rank

Structural evidence

Ligand evidence