Protein profile

KP13_00813

Ribonuclease 3

Genome: KpKP13

Gene: AHE43177.1 rnc Structure source: AlphaFold + ColabFold UniProt A0A0H3GWU8

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Amino acids 226

Annotations 13

Features 30

PDB binders 1

Druggability 0.374

Overview

Basic information about this protein and its source genome.

Accession: KP13_00813
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43177.1 rnc
Status: annotated
Amino acids: 226
Structure source: AlphaFold + ColabFold

3.1.26.3

GO:0004525 Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt. GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0003725 Binding to double-stranded RNA.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 35.065
Human E-value: 9.48e-07
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 96.903
DEG E-value: 8.29e-165
Localization: Cytoplasmic
ColabFold pLDDT: 94.93

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 0.374

Structure A0A0H3GWU8

Pocket Pocket 2

P2Rank 0.02

Structure A0A0H3GWU8

Pocket Pocket 1

ColabFold model

FPocket 0.358 · Pocket 1

P2Rank 0.043 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 202 / 4744 genomes with a hit

Normalized 0.043

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 12 GO

Enzyme Commission (EC)

3.1.26.3

Gene Ontology (GO)

GO:0004525 Catalysis of the endonucleolytic cleavage of RNA with 5'-phosphomonoesters and 3'-OH termini; makes two staggered cuts in both strands of dsRNA, leaving a 3' overhang of 2 nt.
GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0003725 Binding to double-stranded RNA.
GO:0042802 Binding to an identical protein or proteins.
GO:0046872 Binding to a metal ion.
GO:0019843 Binding to a ribosomal RNA.
GO:0006397 Any process involved in the conversion of a primary mRNA transcript into one or more mature mRNA(s) prior to translation into polypeptide.
GO:0010468 Any process that modulates 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).
GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records

Show feature table

Start	End	DB	Term	Name
9	223	PANTHER	PTHR11207	RIBONUCLEASE III
9	223	InterPro	IPR011907	Ribonuclease III
5	159	SUPERFAMILY	SSF69065	RNase III domain-like
5	159	InterPro	IPR036389	Ribonuclease III, endonuclease domain superfamily
4	147	Gene3D	G3DSA:1.10.1520.10	Ribonuclease III domain
4	147	InterPro	IPR036389	Ribonuclease III, endonuclease domain superfamily
4	147	FunFam	G3DSA:1.10.1520.10:FF:000001	Ribonuclease 3
6	128	ProSiteProfiles	PS50142	Ribonuclease III family domain profile.
6	128	InterPro	IPR000999	Ribonuclease III domain
109	223	SUPERFAMILY	SSF54768	dsRNA-binding domain-like
38	46	ProSitePatterns	PS00517	Ribonuclease III family signature.
38	46	InterPro	IPR000999	Ribonuclease III domain
156	223	Pfam	PF00035	Double-stranded RNA binding motif
156	223	InterPro	IPR014720	Double-stranded RNA-binding domain
9	220	Hamap	MF_00104	Ribonuclease 3 [rnc].
9	220	InterPro	IPR011907	Ribonuclease III
208	226	Coils	Coil	Coil
154	224	Gene3D	G3DSA:3.30.160.20	-
21	149	SMART	SM00535	riboneu5
21	149	InterPro	IPR000999	Ribonuclease III domain
20	141	Pfam	PF14622	Ribonuclease-III-like
20	141	InterPro	IPR000999	Ribonuclease III domain
9	223	NCBIfam	TIGR02191	ribonuclease III
155	225	ProSiteProfiles	PS50137	Double stranded RNA-binding domain (dsRBD) profile.
155	225	InterPro	IPR014720	Double-stranded RNA-binding domain
156	224	SMART	SM00358	DRBM_3
156	224	InterPro	IPR014720	Double-stranded RNA-binding domain
21	149	CDD	cd00593	RIBOc
154	225	FunFam	G3DSA:3.30.160.20:FF:000003	Ribonuclease 3
154	210	CDD	cd10845	DSRM_RNAse_III_family

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...

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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_A0A0H3GWU8	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00813	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
2				0.374

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
1				0.358

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.

60 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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
MLI	3LLH	Q15633-2	102.0 Da LogP -3.12 TPSA 80.3	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(=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).

Ligand	UniProt (homolog)	pchembl	MW · LogP · TPSA	Lipinski	PAINS	SMILES
CHEMBL5170759	Q15633	7.98	261.3 Da LogP 2.84 TPSA 61.6	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccc(OC)cc2)oc1C`
CHEMBL5180444	Q15633	7.72	245.3 Da LogP 3.14 TPSA 52.3	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccc(C)cc2)oc1C`
CHEMBL826	Q15633	7.03	320.3 Da LogP 0.66 TPSA 87.5	✓ Ro5	✓ Clean	`CCn1cc(C(=O)O)c(=O)c2cc(F)c(N3CCNCC3)nc21`
CHEMBL5178502	Q15633	6.90	307.3 Da LogP 4.49 TPSA 52.3	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccc(-c3ccccc3)cc2)oc1C`
CHEMBL5175086	Q15633	6.63	310.1 Da LogP 3.59 TPSA 52.3	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccc(Br)cc2)oc1C`
CHEMBL5201452	Q15633	6.17	275.3 Da LogP 3.09 TPSA 61.6	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccc(OC)cc2)oc1CC`
CHEMBL463499	Q15633	—	386.4 Da LogP 4.18 TPSA 66.4	✓ Ro5	✓ Clean	`COc1cc2c(c(O)c1OC)-c1c(cc3c(c1OC)OCO3)C[C@H](C)…`
CHEMBL5092946	Q15633	—	654.8 Da LogP 4.24 TPSA 144.5	1 viol.	✓ Clean	`COC(=O)c1cc2c(c(OC)c1-c1ccc(N(C)C(=O)CCCCCNC(=O…`
CHEMBL5093445	Q15633	—	315.3 Da LogP 2.92 TPSA 66.0	✓ Ro5	✓ Clean	`CNc1ccc(-c2c(C(=O)OC)cc3c(c2OC)OCO3)cc1`

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
ZINC118531710	1.000	261.3 Da LogP 2.84 TPSA 61.6	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccc(OC)cc2)oc1C`
ZINC19594549	1.000	320.3 Da LogP 0.66 TPSA 87.5	✓ Ro5	✓ Clean	`CCn1cc(C(=O)O)c(=O)c2cc(F)c(N3CCNCC3)nc21`
ZINC5000426	0.944	231.3 Da LogP 2.83 TPSA 52.3	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccccc2)oc1C`
ZINC31169950	0.826	386.4 Da LogP 4.18 TPSA 66.4	✓ Ro5	✓ Clean	`COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1O)OCO3)C[C@H](C)…`
ZINC31169953	0.826	386.4 Da LogP 4.18 TPSA 66.4	✓ Ro5	✓ Clean	`COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1O)OCO3)C[C@H](C)…`
ZINC31169956	0.826	386.4 Da LogP 4.18 TPSA 66.4	✓ Ro5	✓ Clean	`COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1O)OCO3)C[C@@H](C…`
ZINC1531882	0.818	400.5 Da LogP 4.49 TPSA 55.4	✓ Ro5	✓ Clean	`COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1OC)OCO3)C[C@@H](…`
ZINC1531911	0.818	400.5 Da LogP 4.49 TPSA 55.4	✓ Ro5	✓ Clean	`COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1OC)OCO3)C[C@H](C…`
ZINC2558151	0.818	400.5 Da LogP 4.49 TPSA 55.4	✓ Ro5	✓ Clean	`COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1OC)OCO3)C[C@@H](…`
ZINC4214303	0.818	400.5 Da LogP 4.49 TPSA 55.4	✓ Ro5	✓ Clean	`COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1OC)OCO3)C[C@H](C…`
ZINC95835986	0.769	247.2 Da LogP 2.45 TPSA 61.6	✓ Ro5	✓ Clean	`COC(=O)c1nc(-c2ccc(OC)cc2)oc1C`
ZINC39200903	0.756	265.7 Da LogP 3.48 TPSA 52.3	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccc(Cl)cc2)oc1C`
ZINC5538657	0.738	260.2 Da LogP 1.29 TPSA 95.4	✓ Ro5	✓ Clean	`Cc1oc(-c2ccccc2)nc1C(=O)OCC(N)=O`
ZINC79006513	0.732	232.2 Da LogP 2.10 TPSA 78.3	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccccc2)oc1N`
ZINC98178285	0.732	251.7 Da LogP 3.17 TPSA 52.3	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccccc2)oc1Cl`
ZINC34633392	0.727	277.3 Da LogP 1.81 TPSA 99.6	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccc(OC)cc2)oc1NN`
ZINC5539480	0.705	321.3 Da LogP 3.69 TPSA 69.4	✓ Ro5	✓ Clean	`Cc1oc(-c2ccccc2)nc1C(=O)OCC(=O)c1ccccc1`
ZINC20357801	0.700	233.2 Da LogP 2.36 TPSA 72.6	✓ Ro5	✓ Clean	`COc1ccc(-c2nc(C(=O)O)c(C)o2)cc1`
ZINC5538644	0.700	217.2 Da LogP 2.44 TPSA 52.3	✓ Ro5	✓ Clean	`COC(=O)c1nc(-c2ccccc2)oc1C`
ZINC1614237	0.698	261.3 Da LogP 2.92 TPSA 61.6	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccccc2)oc1OCC`
ZINC3548527	0.689	301.3 Da LogP 3.42 TPSA 69.4	✓ Ro5	✓ Clean	`Cc1oc(-c2ccccc2)nc1C(=O)OCC(=O)C(C)(C)C`
ZINC5539523	0.688	337.4 Da LogP 4.41 TPSA 61.6	✓ Ro5	✓ Clean	`CCOc1ccccc1COC(=O)c1nc(-c2ccccc2)oc1C`
ZINC1574833	0.682	402.5 Da LogP 4.47 TPSA 66.4	✓ Ro5	✓ Clean	`COc1cc2c(c(O)c1OC)-c1c(cc(OC)c(OC)c1OC)C[C@@H](…`
ZINC1574834	0.682	402.5 Da LogP 4.47 TPSA 66.4	✓ Ro5	✓ Clean	`COc1cc2c(c(O)c1OC)-c1c(cc(OC)c(OC)c1OC)C[C@@H](…`
ZINC1574835	0.682	402.5 Da LogP 4.47 TPSA 66.4	✓ Ro5	✓ Clean	`COc1cc2c(c(O)c1OC)-c1c(cc(OC)c(OC)c1OC)C[C@H](C…`
ZINC1574836	0.682	402.5 Da LogP 4.47 TPSA 66.4	✓ Ro5	✓ Clean	`COc1cc2c(c(O)c1OC)-c1c(cc(OC)c(OC)c1OC)C[C@H](C…`
ZINC34633394	0.682	247.3 Da LogP 1.80 TPSA 90.4	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccccc2)oc1NN`
ZINC95347959	0.682	300.1 Da LogP 4.13 TPSA 52.3	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccc(Cl)c(Cl)c2)oc1C`
ZINC29866093	0.681	313.3 Da LogP 2.95 TPSA 91.2	✓ Ro5	✓ Clean	`CCc1nnc(COC(=O)c2nc(-c3ccccc3)oc2C)o1`
ZINC9613813	0.681	362.3 Da LogP 3.06 TPSA 89.7	✓ Ro5	✓ Clean	`Cc1oc(-c2ccccc2)nc1C(=O)OCN1C(=O)c2ccccc2C1=O`
ZINC5537068	0.680	410.4 Da LogP 3.81 TPSA 111.5	✓ Ro5	✓ Clean	`CCOC(=O)c1c(C)[nH]c(C)c1C(=O)COC(=O)c1nc(-c2ccc…`
ZINC95398607	0.680	327.3 Da LogP 2.71 TPSA 79.4	✓ Ro5	✓ Clean	`COc1ccc(-c2nc(C(=O)OCCn3cccn3)c(C)o2)cc1`
ZINC29345454	0.679	302.3 Da LogP 0.52 TPSA 87.5	✓ Ro5	✓ Clean	`CCn1cc(C(=O)O)c(=O)c2ccc(N3CCNCC3)nc21`
ZINC26468329	0.679	386.4 Da LogP 1.77 TPSA 87.5	✓ Ro5	✓ Clean	`O=C(O)c1cn(-c2ccc(F)cc2)c2nc(N3CCNCC3)c(F)cc2c1…`
ZINC41438746	0.675	282.1 Da LogP 3.11 TPSA 63.3	✓ Ro5	✓ Clean	`Cc1oc(-c2ccc(Br)cc2)nc1C(=O)O`
ZINC3552312	0.674	361.4 Da LogP 4.06 TPSA 91.2	✓ Ro5	✓ Clean	`Cc1oc(-c2ccccc2)nc1C(=O)OCc1nnc(-c2ccccc2)o1`
ZINC98178291	0.674	327.8 Da LogP 4.84 TPSA 52.3	✓ Ro5	✓ Clean	`CCOC(=O)c1nc(-c2ccc(Cl)cc2)oc1-c1ccccc1`
ZINC14468058	0.667	279.3 Da LogP 3.87 TPSA 52.3	✓ Ro5	✓ Clean	`Cc1oc(-c2ccccc2)nc1C(=O)Oc1ccccc1`
ZINC5537516	0.667	349.4 Da LogP 4.25 TPSA 69.4	✓ Ro5	✓ Clean	`CCc1ccc(C(=O)COC(=O)c2nc(-c3ccccc3)oc2C)cc1`
ZINC85225013	0.667	248.2 Da LogP 1.92 TPSA 74.5	✓ Ro5	✓ Clean	`CCOC(=O)c1nnc(-c2ccc(OC)cc2)o1`
ZINC14184458	0.660	299.3 Da LogP 2.70 TPSA 91.2	✓ Ro5	✓ Clean	`Cc1nnc(COC(=O)c2nc(-c3ccccc3)oc2C)o1`
ZINC5537772	0.660	303.3 Da LogP 1.00 TPSA 124.5	✓ Ro5	✓ Clean	`Cc1oc(-c2ccccc2)nc1C(=O)OCC(=O)NC(N)=O`
ZINC5538649	0.660	327.8 Da LogP 4.66 TPSA 52.3	✓ Ro5	✓ Clean	`Cc1oc(-c2ccccc2)nc1C(=O)OCc1ccc(Cl)cc1`
ZINC39290862	0.654	270.6 Da LogP 1.91 TPSA 72.2	✓ Ro5	✓ Clean	`CCn1cc(C(=O)O)c(=O)c2cc(F)c(Cl)nc21`
ZINC5538670	0.653	376.4 Da LogP 3.10 TPSA 89.7	✓ Ro5	✓ Clean	`Cc1oc(-c2ccccc2)nc1C(=O)OCCN1C(=O)c2ccccc2C1=O`
ZINC11616528	0.648	416.5 Da LogP 3.60 TPSA 75.6	✓ Ro5	✓ Clean	`COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1OC)OCO3)C[C@H](C…`
ZINC15262532	0.648	416.5 Da LogP 3.98 TPSA 75.6	✓ Ro5	✓ Clean	`COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1OC)OCO3)C[C@H](C…`
ZINC15262534	0.648	416.5 Da LogP 3.98 TPSA 75.6	✓ Ro5	✓ Clean	`COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1OC)OCO3)C[C@H](C…`
ZINC15262538	0.648	416.5 Da LogP 3.98 TPSA 75.6	✓ Ro5	✓ Clean	`COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1OC)OCO3)C[C@H](C…`
ZINC2388377	0.648	416.5 Da LogP 3.60 TPSA 75.6	✓ Ro5	✓ Clean	`COc1cc2c(c(OC)c1OC)-c1c(cc3c(c1OC)OCO3)C[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.