Protein profile

KP13_00538

Ribonuclease R

Genome: KpKP13

Gene: rnr AHE46730.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GI27

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Amino acids 810

Annotations 9

Features 47

PDB binders 1

Druggability 0.555

Overview

Basic information about this protein and its source genome.

Accession: KP13_00538
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rnr AHE46730.1
Status: annotated
Amino acids: 810
Structure source: AlphaFold + ColabFold

3.1.13.1

GO:0003676 Binding to a nucleic acid. GO:0016070 The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0004518 Catalysis of the cleavage of ester linkages within nucleic acids. GO:0004540 Catalysis of the cleavage of phosphodiester bonds in chains of RNA. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 34.127
Human E-value: 1.06e-08
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 93.082
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 87.64

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 0.555

Structure A0A0H3GI27

Pocket Pocket 66

P2Rank 0.851

Structure A0A0H3GI27

Pocket Pocket 1

ColabFold model

FPocket 0.095 · Pocket 58

P2Rank 0.803 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 153 / 4744 genomes with a hit

Normalized 0.032

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

3.1.13.1

Gene Ontology (GO)

GO:0003676 Binding to a nucleic acid.
GO:0016070 The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
GO:0003723 Binding to an RNA molecule or a portion thereof.
GO:0004518 Catalysis of the cleavage of ester linkages within nucleic acids.
GO:0004540 Catalysis of the cleavage of phosphodiester bonds in chains of RNA.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0008859 Catalysis of the reaction: RNA + H2O = 5'-phosphomononucleotides. Cleaves RNA in the 3' to 5' direction.
GO:0006402 The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.

Sequence Features

Domain/signature hits from InterPro and related databases.

47 records

Show feature table

Start	End	DB	Term	Name
163	738	PANTHER	PTHR23355	RIBONUCLEASE
67	145	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
67	145	InterPro	IPR012340	Nucleic acid-binding, OB-fold
642	725	SMART	SM00316	S1_6
642	725	InterPro	IPR022967	RNA-binding domain, S1
45	65	Coils	Coil	Coil
645	756	FunFam	G3DSA:2.40.50.140:FF:000161	Ribonuclease R
19	725	NCBIfam	TIGR02063	ribonuclease R
19	725	InterPro	IPR011805	Ribonuclease R
86	145	SMART	SM00357	csp_8
86	145	InterPro	IPR011129	Cold shock domain
731	810	MobiDBLite	mobidb-lite	consensus disorder prediction
765	781	MobiDBLite	mobidb-lite	consensus disorder prediction
164	238	Pfam	PF17876	Cold shock domain
164	238	InterPro	IPR040476	RNase II/RNase R, cold shock domain
67	725	NCBIfam	TIGR00358	VacB/RNase II family 3'-5' exoribonuclease
67	725	InterPro	IPR004476	Ribonuclease II/ribonuclease R
643	725	CDD	cd04471	S1_RNase_R
644	725	ProSiteProfiles	PS50126	S1 domain profile.
644	725	InterPro	IPR003029	S1 domain
641	723	Pfam	PF00575	S1 RNA binding domain
641	723	InterPro	IPR003029	S1 domain
87	144	Pfam	PF08206	Ribonuclease B OB domain
87	144	InterPro	IPR013223	Ribonuclease B, N-terminal OB domain
555	579	ProSitePatterns	PS01175	Ribonuclease II family signature.
555	579	InterPro	IPR022966	Ribonuclease II/R, conserved site
67	147	FunFam	G3DSA:2.40.50.140:FF:000124	Ribonuclease R
23	85	Pfam	PF08461	Ribonuclease R winged-helix domain
23	85	InterPro	IPR013668	Ribonuclease R winged-helix domain
403	423	Coils	Coil	Coil
260	587	Pfam	PF00773	RNB domain
260	587	InterPro	IPR001900	Ribonuclease II/R
260	588	SMART	SM00955	RNB_2
260	588	InterPro	IPR001900	Ribonuclease II/R
222	641	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
222	641	InterPro	IPR012340	Nucleic acid-binding, OB-fold
644	724	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
644	724	InterPro	IPR012340	Nucleic acid-binding, OB-fold
138	235	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
138	235	InterPro	IPR012340	Nucleic acid-binding, OB-fold
69	148	Gene3D	G3DSA:2.40.50.140	-
69	148	InterPro	IPR012340	Nucleic acid-binding, OB-fold
645	750	Gene3D	G3DSA:2.40.50.140	-
645	750	InterPro	IPR012340	Nucleic acid-binding, OB-fold
733	747	MobiDBLite	mobidb-lite	consensus disorder prediction
38	725	Hamap	MF_01895	Ribonuclease R [rnr].
38	725	InterPro	IPR011805	Ribonuclease R

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_A0A0H3GI27	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_00538	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
66				0.555
71				0.019
40				0.003
6				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	24.26	0.851
2	3.46	0.1
3	2.59	0.06
4	2.29	0.047
5	2.08	0.039

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	8.34	0.445
2	5.14	0.236
3	2.67	0.079
4	2.18	0.052
5	1.39	0.017

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.

31 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
VGL	4NNI	P9WH43	124.1 Da LogP 0.17 TPSA 63.1	✓ Ro5	✓ Clean	`c1cnc(cn1)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).

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
ZINC20357720	0.581	228.2 Da LogP 1.41 TPSA 80.1	✓ Ro5	✓ Clean	`O=C(O)c1ccccc1C(=O)c1cnccn1`
ZINC2749775	0.552	272.3 Da LogP -0.57 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NCCNC(=O)c1cnccn1)c1cnccn1`
ZINC20496347	0.548	219.3 Da LogP 1.88 TPSA 46.1	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCCCCCC1`
ZINC5705248	0.548	205.3 Da LogP 1.49 TPSA 46.1	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCCCCC1`
ZINC69048726	0.548	201.2 Da LogP 1.24 TPSA 76.0	✓ Ro5	✓ Clean	`O=C(O)c1ccc(-c2cnccn2)cn1`
ZINC12360654	0.545	207.2 Da LogP 1.30 TPSA 76.0	✓ Ro5	✓ Clean	`O=C(O)c1csc(-c2cnccn2)n1`
ZINC26423456	0.543	250.2 Da LogP 0.88 TPSA 105.1	✓ Ro5	✓ Clean	`O=C(O)c1csc(NC(=O)c2cnccn2)n1`
ZINC2580774	0.531	216.3 Da LogP 2.41 TPSA 42.9	✓ Ro5	✓ Clean	`O=C(Sc1ccccc1)c1cnccn1`
ZINC4749098	0.529	243.2 Da LogP 1.43 TPSA 92.2	✓ Ro5	✓ Clean	`O=C(O)c1ccc(NC(=O)c2cnccn2)cc1`
ZINC2747329	0.516	300.3 Da LogP 0.21 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NCCCCNC(=O)c1cnccn1)c1cnccn1`
ZINC2747452	0.516	286.3 Da LogP -0.18 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NCCCNC(=O)c1cnccn1)c1cnccn1`
ZINC19092783	0.515	205.2 Da LogP 0.28 TPSA 63.2	✓ Ro5	✓ Clean	`O=C1CCN(C(=O)c2cnccn2)CC1`
ZINC40542019	0.515	209.3 Da LogP 0.67 TPSA 46.1	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCSCC1`
ZINC54792854	0.515	202.2 Da LogP 0.63 TPSA 88.9	✓ Ro5	✓ Clean	`O=C(O)c1ccnc(-c2cnccn2)n1`
ZINC74212868	0.515	201.2 Da LogP 1.24 TPSA 76.0	✓ Ro5	✓ Clean	`O=C(O)c1cccc(-c2cnccn2)n1`
ZINC79435988	0.515	209.2 Da LogP -0.32 TPSA 83.4	✓ Ro5	✓ Clean	`CN(CC(=O)O)CC(=O)c1cnccn1`
ZINC96047318	0.515	366.4 Da LogP 1.43 TPSA 92.2	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCC2(CC1)CCN(C(=O)c1cnccn1)CC2`
ZINC21953682	0.514	235.2 Da LogP 0.41 TPSA 83.4	✓ Ro5	✓ Clean	`O=C(O)C1CCN(C(=O)c2cnccn2)CC1`
ZINC12982005	0.500	221.2 Da LogP 0.17 TPSA 83.4	✓ Ro5	✓ Clean	`O=C(O)[C@@H]1CCCN1C(=O)c1cnccn1`
ZINC13208295	0.500	200.2 Da LogP 1.12 TPSA 67.8	✓ Ro5	✓ Clean	`O=C(Nc1ccncc1)c1cnccn1`
ZINC20280834	0.500	221.2 Da LogP 0.17 TPSA 83.4	✓ Ro5	✓ Clean	`O=C(O)[C@H]1CCCN1C(=O)c1cnccn1`
ZINC2755537	0.500	328.4 Da LogP 0.99 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NCCCCCCNC(=O)c1cnccn1)c1cnccn1`
ZINC32004931	0.500	202.2 Da LogP 1.85 TPSA 42.9	✓ Ro5	✓ Clean	`O=C(c1ccc(F)cc1)c1cnccn1`
ZINC35110503	0.500	207.2 Da LogP 0.07 TPSA 66.3	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCC(O)CC1`
ZINC375500	0.500	326.4 Da LogP 0.74 TPSA 109.8	✓ Ro5	✓ Clean	`O=C(NC1CCC(NC(=O)c2cnccn2)CC1)c1cnccn1`
ZINC37658100	0.500	218.6 Da LogP 2.36 TPSA 42.9	✓ Ro5	✓ Clean	`O=C(c1ccc(Cl)cc1)c1cnccn1`
ZINC54856994	0.500	202.2 Da LogP 0.63 TPSA 88.9	✓ Ro5	✓ Clean	`O=C(O)c1cnc(-c2cnccn2)nc1`
ZINC646774339	0.500	231.3 Da LogP 1.74 TPSA 46.1	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CCC(C2CC2)CC1`
ZINC77101491	0.500	207.2 Da LogP -0.37 TPSA 83.4	✓ Ro5	✓ Clean	`O=C(O)C1CN(C(=O)c2cnccn2)C1`
ZINC96053972	0.500	324.3 Da LogP 0.11 TPSA 92.2	✓ Ro5	✓ Clean	`O=C(c1cnccn1)N1CC2CN(C(=O)c3cnccn3)CC2C1`

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.