KpATCC43816 Protein target profile

ribonuclease T

Accession: VK055_0486

Gene: AIK79109.1 rnt 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GP72

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Length 215

Pocket druggability (P2Rank · AlphaFold DB model) 0.804

Direct ligand evidence 0 52 total records

Functional annotation 0 EC 3 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

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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: 3.9% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 88.732 Higher values support similarity to known essential genes.
DEG E-value: 6.55e-143 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 95.14 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) 0.804

Structure A0A0H3GP72

Pocket Pocket 1

Druggability (FPocket) 0.606

Structure A0A0H3GP72

Pocket Pocket 3

ColabFold model

P2Rank 0.863 · Pocket 1

FPocket 0.675 · Pocket 2

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 186 / 4744 genomes with a hit

Prevalence 3.9%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSENAQLNGLCDRFRGFYPVVIDVETAGFNAKTDALLEIAAITLKMDEHGWLMPDETLHFHVEPFEGANLQPEALAFNGINPHDPQRGAVSEYDALHAIFKMVRKGMKESDCSRAIMVAHNATFDHSFTMTAAERAGLKRNPFHPFVTFDTAALSGLALGQTVLSKACIAAGMPFDGAQAHSALYDTEQTAQLFCEIVNRWKRLGGWPLPVATPE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization: Cytoplasmic

Gene Ontology (GO)

GO:0004540 Catalysis of the cleavage of phosphodiester bonds in chains of RNA.
GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
GO:0003676 Binding to a nucleic acid.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

16 records

Show feature table

Start	End	DB	Term	Name
12	207	SUPERFAMILY	SSF53098	Ribonuclease H-like
12	207	InterPro	IPR012337	Ribonuclease H-like superfamily
20	204	PANTHER	PTHR30231	DNA POLYMERASE III SUBUNIT EPSILON
20	194	Pfam	PF00929	Exonuclease
20	194	InterPro	IPR013520	Exonuclease, RNase T/DNA polymerase III
18	203	SMART	SM00479	exoiiiendus
18	203	InterPro	IPR013520	Exonuclease, RNase T/DNA polymerase III
9	213	Gene3D	G3DSA:3.30.420.10	-
9	213	InterPro	IPR036397	Ribonuclease H superfamily
13	201	CDD	cd06134	RNaseT
13	201	InterPro	IPR005987	Ribonuclease T
9	214	FunFam	G3DSA:3.30.420.10:FF:000009	Ribonuclease T
1	215	Hamap	MF_00157	Ribonuclease T [rnt].
1	215	InterPro	IPR005987	Ribonuclease T
10	208	NCBIfam	TIGR01298	ribonuclease T
10	208	InterPro	IPR005987	Ribonuclease T

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

0.804

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Surrounding area

Pocket 2 P2Rank #2

0.183

Likely same site as FPocket 3 4.3 Å 9 shared residues 100% of smaller site

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Surrounding area

Pocket 3 P2Rank #3

0.015

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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 #3

0.606

Likely same site as P2Rank 2 4.3 Å 9 shared residues 100% of smaller site

Show in viewer

Surrounding area

Residue sets

UniProt: Active site:181-181 Proton donor/acceptor

UniProt: Binding site:181-181

UniProt: Binding site:186-186

UniProt: Binding site:23-23

UniProt: Binding site:25-25

UniProt: Site:124-124 Important for substrate binding and specificity

UniProt: Site:146-146 Important for substrate binding and specificity

UniProt: Site:29-29 Important for substrate binding and specificity

UniProt: Site:77-77 Important for substrate binding and specificity

Binding pockets · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1

0.863

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Surrounding area

Pocket 2 P2Rank #2

0.116

Likely same site as FPocket 2 4.6 Å 9 shared residues 100% of smaller site

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Surrounding area

Pocket 3 P2Rank #3

0.004

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Surrounding area

Residue sets

UniProt: Active site:181-181 Proton donor/acceptor

UniProt: Binding site:181-181

UniProt: Binding site:186-186

UniProt: Binding site:23-23

UniProt: Binding site:25-25

UniProt: Site:124-124 Important for substrate binding and specificity

UniProt: Site:146-146 Important for substrate binding and specificity

UniProt: Site:29-29 Important for substrate binding and specificity

UniProt: Site:77-77 Important for substrate binding and specificity

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_A0A0H3GP72	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_0486	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

Bioactivity evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 2 records from similar proteins

Structural ligands 0 0 loaded crystals

Measured bioactivity 2 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

CHEMBL395814 ChEMBL via homolog 396.4 Da · LogP 3.70 · TPSA 160.9 Open detail ChEMBL

QU4 ChEMBL via homolog Detail ChEMBL

ZINC3833863 ZINC proposed compound · Tanimoto 1.000 Detail ZINC

ZINC7814925 ZINC proposed compound · Tanimoto 0.758 Detail ZINC

ZINC2054344316 ZINC proposed compound · Tanimoto 0.756 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.

No PDB ligands found through similar proteins.

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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL395814 ChEMBL	P30014	—	396.4 Da LogP 3.70 TPSA 160.9	✓ Ro5	✓ Clean	`O=C(O)c1cc(SSc2ccc([N+](=O)[O-])c(C(=O)O)c2)ccc…`
QU4 ChEMBL	P30014	—	422.3 Da LogP 2.45 TPSA 169.4	✓ Ro5	✓ Clean	`c1cc(c(cc1C(=C2C=CC(=O)C(=C2)C(=O)O)c3ccc(c(c3)…`

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
ZINC3833863 ZINC	1.000	422.3 Da LogP 2.45 TPSA 169.4	✓ Ro5	✓ Clean	`O=C(O)C1=CC(=C(c2ccc(O)c(C(=O)O)c2)c2ccc(O)c(C(…`
ZINC7814925 ZINC	0.758	213.2 Da LogP 2.01 TPSA 80.4	✓ Ro5	✓ Clean	`CSc1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC2054344316 ZINC	0.756	300.3 Da LogP 2.01 TPSA 111.9	✓ Ro5	✓ Clean	`CC(=C1C=CC(=O)C(C(=O)O)=C1)c1ccc(O)c(C(=O)O)c1`
ZINC28092924 ZINC	0.756	300.3 Da LogP 2.01 TPSA 111.9	✓ Ro5	✓ Clean	`C/C(=C1/C=CC(=O)C(C(=O)O)=C1)c1ccc(O)c(C(=O)O)c1`
ZINC36748824 ZINC	0.756	300.3 Da LogP 2.01 TPSA 111.9	✓ Ro5	✓ Clean	`C/C(=C1\C=CC(=O)C(C(=O)O)=C1)c1ccc(O)c(C(=O)O)c1`
ZINC13275004 ZINC	0.676	309.7 Da LogP 4.10 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(Sc2ccc(Cl)cc2)ccc1[N+](=O)[O-]`
ZINC64708385 ZINC	0.644	467.4 Da LogP 0.44 TPSA 214.5	1 viol.	✓ Clean	`NOC(=O)C1=CC(=C(c2ccc(O)c(C(=O)ON)c2)c2ccc(O)c(…`
ZINC2575270 ZINC	0.636	211.1 Da LogP 0.99 TPSA 117.7	✓ Ro5	✓ Clean	`O=C(O)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC4404106 ZINC	0.636	212.1 Da LogP 1.20 TPSA 123.6	✓ Ro5	✓ Clean	`O=C(O)c1cc([N+](=O)[O-])ccc1[N+](=O)[O-]`
ZINC2565533 ZINC	0.633	256.1 Da LogP 0.90 TPSA 160.9	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)c([N+](=O)[O-])cc1[N+](=O)[O-]`
ZINC1689765 ZINC	0.618	201.6 Da LogP 1.95 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(Cl)ccc1[N+](=O)[O-]`
ZINC1692553 ZINC	0.618	246.0 Da LogP 2.06 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(Br)ccc1[N+](=O)[O-]`
ZINC34143793 ZINC	0.618	293.0 Da LogP 1.90 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(I)ccc1[N+](=O)[O-]`
ZINC19801481 ZINC	0.583	223.2 Da LogP 2.59 TPSA 80.4	✓ Ro5	✓ Clean	`CC(C)(C)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC1870293 ZINC	0.568	247.1 Da LogP 0.10 TPSA 138.0	✓ Ro5	✓ Clean	`O=C(O)c1cc(P(=O)(O)O)ccc1[N+](=O)[O-]`
ZINC197020550 ZINC	0.568	246.2 Da LogP -0.06 TPSA 140.6	✓ Ro5	✓ Clean	`NS(=O)(=O)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC19845324 ZINC	0.568	210.2 Da LogP 1.36 TPSA 83.7	✓ Ro5	✓ Clean	`CN(C)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC34202985 ZINC	0.568	213.2 Da LogP 2.01 TPSA 80.4	✓ Ro5	✓ Clean	`CSc1ccc(C(=O)O)c([N+](=O)[O-])c1`
ZINC59269089 ZINC	0.568	245.2 Da LogP 0.70 TPSA 114.6	✓ Ro5	✓ Clean	`CS(=O)(=O)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC72338575 ZINC	0.568	235.1 Da LogP 2.31 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(F)(F)F)ccc1[N+](=O)[O-]`
ZINC3845121 ZINC	0.559	226.1 Da LogP 0.57 TPSA 143.8	✓ Ro5	✓ Clean	`Nc1cc([N+](=O)[O-])c(C(=O)O)cc1C(=O)O`
ZINC4529802 ZINC	0.559	324.9 Da LogP 2.82 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(Br)c(Br)cc1[N+](=O)[O-]`
ZINC4284655 ZINC	0.553	224.2 Da LogP 1.25 TPSA 109.5	✓ Ro5	✓ Clean	`CC(=O)Nc1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC346060 ZINC	0.543	245.6 Da LogP 1.64 TPSA 117.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(C(=O)O)c([N+](=O)[O-])cc1Cl`
ZINC14985550 ZINC	0.538	225.2 Da LogP 1.08 TPSA 106.7	✓ Ro5	✓ Clean	`COC(=O)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC15443713 ZINC	0.538	236.2 Da LogP 1.89 TPSA 83.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(N2CCCC2)ccc1[N+](=O)[O-]`
ZINC1610707 ZINC	0.538	269.3 Da LogP 3.46 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(/C=C/c2ccccc2)ccc1[N+](=O)[O-]`
ZINC19400583 ZINC	0.538	225.2 Da LogP 2.08 TPSA 89.7	✓ Ro5	✓ Clean	`CC(C)Oc1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC22163863 ZINC	0.538	259.2 Da LogP 3.09 TPSA 89.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(Oc2ccccc2)ccc1[N+](=O)[O-]`
ZINC5160214 ZINC	0.538	269.3 Da LogP 3.46 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(/C=C\c2ccccc2)ccc1[N+](=O)[O-]`
ZINC16698051 ZINC	0.528	293.0 Da LogP 1.90 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)cc1[N+](=O)[O-]`
ZINC39263556 ZINC	0.528	217.2 Da LogP 2.45 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc2ccccc2cc1[N+](=O)[O-]`
ZINC13179356 ZINC	0.525	250.3 Da LogP 2.28 TPSA 83.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(N2CCCCC2)ccc1[N+](=O)[O-]`
ZINC16158718 ZINC	0.525	251.1 Da LogP 2.19 TPSA 89.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(OC(F)(F)F)ccc1[N+](=O)[O-]`
ZINC16385345 ZINC	0.525	208.1 Da LogP 2.23 TPSA 129.2	✓ Ro5	Alert	`[N-]=[N+]=Nc1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC19735959 ZINC	0.525	264.3 Da LogP 2.67 TPSA 83.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(N2CCCCCC2)ccc1[N+](=O)[O-]`
ZINC19844564 ZINC	0.525	238.2 Da LogP 2.14 TPSA 83.7	✓ Ro5	✓ Clean	`CCN(CC)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC22214518 ZINC	0.525	211.2 Da LogP 1.69 TPSA 89.7	✓ Ro5	✓ Clean	`CCOc1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC19845080 ZINC	0.524	293.3 Da LogP 0.96 TPSA 104.0	✓ Ro5	✓ Clean	`CC(=O)N1CCN(c2ccc([N+](=O)[O-])c(C(=O)O)c2)CC1`
ZINC12671061 ZINC	0.520	346.4 Da LogP 4.29 TPSA 74.6	✓ Ro5	✓ Clean	`CC1=C/C(=C(/c2ccc(O)c(C)c2)c2ccccc2C(=O)O)C=CC1…`
ZINC3953836 ZINC	0.520	346.4 Da LogP 4.29 TPSA 74.6	✓ Ro5	✓ Clean	`CC1=C/C(=C(\c2ccc(O)c(C)c2)c2ccccc2C(=O)O)C=CC1…`
ZINC2569918 ZINC	0.514	203.1 Da LogP 1.57 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(F)c(F)cc1[N+](=O)[O-]`
ZINC32169655 ZINC	0.514	236.0 Da LogP 2.60 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(Cl)c(Cl)cc1[N+](=O)[O-]`
ZINC13179470 ZINC	0.512	252.3 Da LogP 2.53 TPSA 83.7	✓ Ro5	✓ Clean	`CCCCN(C)c1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC12503280 ZINC	0.510	302.2 Da LogP 1.01 TPSA 136.3	✓ Ro5	Alert	`O=C(O)C1=C/C(=N\Nc2ccc(O)c(C(=O)O)c2)C=CC1=O`
ZINC4565385 ZINC	0.510	356.4 Da LogP 3.24 TPSA 111.1	✓ Ro5	✓ Clean	`Cn1c(Sc2ccc([N+](=O)[O-])c(C(=O)O)c2)nnc1-c1ccc…`
ZINC95536736 ZINC	0.510	302.2 Da LogP 1.01 TPSA 136.3	✓ Ro5	Alert	`O=C(O)C1=C/C(=N/Nc2ccc(O)c(C(=O)O)c2)C=CC1=O`
ZINC1701223 ZINC	0.500	302.2 Da LogP 1.73 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(c1ccc(O)c(C(=O)O)c1)c1ccc(O)c(C(=O)O)c1`
ZINC1715466 ZINC	0.500	225.2 Da LogP 1.30 TPSA 117.7	✓ Ro5	✓ Clean	`Cc1cc(C(=O)O)c([N+](=O)[O-])cc1C(=O)O`
ZINC26514919 ZINC	0.500	223.2 Da LogP 1.86 TPSA 89.7	✓ Ro5	✓ Clean	`C=CCOc1ccc([N+](=O)[O-])c(C(=O)O)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 A0A0H3GP72

Chemistry

ChEMBL CHEMBL395814 ChEMBL QU4