Protein profile

KP13_05148

Ribonuclease T

Genome: KpKP13

Gene: AHE44267.1 rnt Structure source: AlphaFold + ColabFold UniProt A0A0H3GP72

Export view

Amino acids 215

Annotations 3

Features 16

PDB binders 0

Druggability 0.606

Overview

Basic information about this protein and its source genome.

Accession: KP13_05148
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE44267.1 rnt
Status: annotated
Amino acids: 215
Structure source: AlphaFold + ColabFold

GO:0003676 Binding to a nucleic acid. 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.

Target profile

Computed evidence for target prioritization.

Human off-target: No hit
Human identity (%): 0.0
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 88.732
DEG E-value: 6.55e-143
Localization: Cytoplasmic
ColabFold pLDDT: 95.14

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.606

Structure A0A0H3GP72

Pocket Pocket 3

P2Rank 0.804

Structure A0A0H3GP72

Pocket Pocket 1

ColabFold model

FPocket 0.738 · Pocket 2

P2Rank 0.851 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 186 / 4744 genomes with a hit

Normalized 0.039

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Gene Ontology (GO)

GO:0003676 Binding to a nucleic acid.
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.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records

Show feature table

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

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

Legend High Medium Low

Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GP72	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_05148	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
3				0.606
9				0.02
10				0.005
1				0.0

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Score	Probability
1	21.09	0.804
2	4.94	0.183
3	1.43	0.015

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
2				0.738

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				16.19	0.772
2				4.35	0.181

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

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, 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	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	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	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	0.758	213.2 Da LogP 2.01 TPSA 80.4	✓ Ro5	✓ Clean	`CSc1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC2054344316	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	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	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	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	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	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	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	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	0.618	201.6 Da LogP 1.95 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(Cl)ccc1[N+](=O)[O-]`
ZINC1692553	0.618	246.0 Da LogP 2.06 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(Br)ccc1[N+](=O)[O-]`
ZINC34143793	0.618	293.0 Da LogP 1.90 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc(I)ccc1[N+](=O)[O-]`
ZINC19801481	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	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	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	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	0.568	213.2 Da LogP 2.01 TPSA 80.4	✓ Ro5	✓ Clean	`CSc1ccc(C(=O)O)c([N+](=O)[O-])c1`
ZINC59269089	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	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	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	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	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	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	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	0.538	236.2 Da LogP 1.89 TPSA 83.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(N2CCCC2)ccc1[N+](=O)[O-]`
ZINC1610707	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	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	0.538	259.2 Da LogP 3.09 TPSA 89.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(Oc2ccccc2)ccc1[N+](=O)[O-]`
ZINC5160214	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	0.528	293.0 Da LogP 1.90 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1ccc(I)cc1[N+](=O)[O-]`
ZINC39263556	0.528	217.2 Da LogP 2.45 TPSA 80.4	✓ Ro5	✓ Clean	`O=C(O)c1cc2ccccc2cc1[N+](=O)[O-]`
ZINC13179356	0.525	250.3 Da LogP 2.28 TPSA 83.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(N2CCCCC2)ccc1[N+](=O)[O-]`
ZINC16158718	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	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	0.525	264.3 Da LogP 2.67 TPSA 83.7	✓ Ro5	✓ Clean	`O=C(O)c1cc(N2CCCCCC2)ccc1[N+](=O)[O-]`
ZINC19844564	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	0.525	211.2 Da LogP 1.69 TPSA 89.7	✓ Ro5	✓ Clean	`CCOc1ccc([N+](=O)[O-])c(C(=O)O)c1`
ZINC19845080	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	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	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	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	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	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	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	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	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	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	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	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.