Protein profile

KP13_02970

Ribonuclease G

Genome: KpKP13

Gene: rng AHE42427.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H3P3

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Amino acids 489

Annotations 4

Features 20

PDB binders 1

Druggability 0.476

Overview

Basic information about this protein and its source genome.

Accession: KP13_02970
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: rng AHE42427.1
Status: annotated
Amino acids: 489
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. GO:0003723 Binding to an RNA molecule or a portion thereof.

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 (%): 53.288
DEG E-value: 6.31e-155
Localization: Cytoplasmic
ColabFold pLDDT: 89.19

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 0.476

Structure A0A0H3H3P3

Pocket Pocket 35

P2Rank 0.546

Structure A0A0H3H3P3

Pocket Pocket 1

ColabFold model

FPocket 0.418 · Pocket 45

P2Rank 0.263 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 227 / 4744 genomes with a hit

Normalized 0.048

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 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.
GO:0003723 Binding to an RNA molecule or a portion thereof.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records

Show feature table

Start	End	DB	Term	Name
38	109	Pfam	PF00575	S1 RNA binding domain
38	109	InterPro	IPR003029	S1 domain
403	489	Gene3D	G3DSA:3.40.1260.20	Ribonuclease E, catalytic domain
39	128	ProSiteProfiles	PS50126	S1 domain profile.
39	128	InterPro	IPR003029	S1 domain
37	122	SMART	SM00316	S1_6
37	122	InterPro	IPR022967	RNA-binding domain, S1
32	128	CDD	cd04453	S1_RNase_E
31	127	Gene3D	G3DSA:2.40.50.140	-
31	127	InterPro	IPR012340	Nucleic acid-binding, OB-fold
13	426	NCBIfam	TIGR00757	Rne/Rng family ribonuclease
13	426	InterPro	IPR004659	Ribonuclease E/G
39	128	SUPERFAMILY	SSF50249	Nucleic acid-binding proteins
39	128	InterPro	IPR012340	Nucleic acid-binding, OB-fold
403	489	FunFam	G3DSA:3.40.1260.20:FF:000001	Ribonuclease G Rng
4	487	PANTHER	PTHR30001	RIBONUCLEASE
4	487	InterPro	IPR004659	Ribonuclease E/G
31	127	FunFam	G3DSA:2.40.50.140:FF:000028	Ribonuclease G
124	393	Pfam	PF10150	Ribonuclease E/G family
124	393	InterPro	IPR019307	RNA-binding protein AU-1/Ribonuclease E/G

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_A0A0H3H3P3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_02970	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
35				0.476
46				0.098
20				0.0
40				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	11.93	0.546
2	7.51	0.332
3	5.17	0.196
4	3.02	0.079
5	2.85	0.072

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
45				0.418

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	4.48	0.191
2	2.1	0.048
3	1.84	0.035
4	0.82	0.003

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.

51 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
U	6G63	P21513	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…`

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
ZINC12503831	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]2…`
ZINC12503833	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H]…`
ZINC13512000	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC1532538	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC2026984	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H]…`
ZINC2123545	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC2606131	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC36377965	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@H](O)[C@@H…`
ZINC3870257	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC3870258	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@…`
ZINC3870259	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@@…`
ZINC3870260	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@@H](O)[C@…`
ZINC9235501	1.000	324.2 Da LogP -2.73 TPSA 171.3	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](COP(=O)(O)O)[C@H](O)[C@H…`
ZINC35636069	0.830	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)OP(=O)(O)O)[…`
ZINC40655887	0.830	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)OP(=O)(O)O)[…`
ZINC40655889	0.830	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC44460318	0.830	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC4490939	0.830	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC8585026	0.830	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC8585028	0.830	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O…`
ZINC8585030	0.830	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O)…`
ZINC8585032	0.830	404.2 Da LogP -2.62 TPSA 217.8	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)OP(=O)(O)O…`
ZINC12959005	0.796	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)O[P@](=O)(O)…`
ZINC12959016	0.796	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@](=O)(O)O[P@](=O)(O…`
ZINC13548378	0.796	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC25726233	0.796	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@](=O)(O)O[P@](=O)(O)…`
ZINC3861755	0.796	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875255	0.796	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875256	0.796	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)…`
ZINC3875257	0.796	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC3875258	0.796	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@@H](CO[P@@](=O)(O)O[P@@](=O)…`
ZINC88466482	0.796	484.1 Da LogP -2.50 TPSA 264.4	2 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@@](=O)(O)O[P@@](=O)(…`
ZINC13517211	0.787	340.2 Da LogP -1.37 TPSA 154.2	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](COP(=O)(O)O)[C@@H](O)[C@H…`
ZINC207686398	0.745	438.2 Da LogP -1.91 TPSA 208.6	1 viol.	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)C(F)(F)P(=O)…`
ZINC71766855	0.717	393.3 Da LogP -2.39 TPSA 163.5	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2O[C@H](CO[P@](=O)(O)N3CCOCC3)[C@…`
ZINC13514392	0.694	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)…`
ZINC1532629	0.694	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c…`
ZINC3869888	0.694	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(…`
ZINC3869889	0.694	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=…`
ZINC3869890	0.694	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(…`
ZINC4228260	0.694	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(…`
ZINC6524723	0.694	308.2 Da LogP -1.71 TPSA 151.1	✓ Ro5	✓ Clean	`O=c1ccn([C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c…`
ZINC102211562	0.691	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@H]1…`
ZINC110347779	0.691	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC110347782	0.691	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC97976147	0.691	490.3 Da LogP -1.89 TPSA 206.8	1 viol.	✓ Clean	`C[N+](C)(C)CCO[P@@](=O)(O)O[P@@](=O)(O)OC[C@@H]…`
ZINC231393132	0.688	287.2 Da LogP -2.75 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)OC[C@@H]1O[C@H](n2ccc(=O)[nH]c2=O)[C@H](O…`
ZINC5104173	0.688	287.2 Da LogP -2.75 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)OC[C@@H]1O[C@@H](n2ccc(=O)[nH]c2=O)[C@H](…`
ZINC5104174	0.688	287.2 Da LogP -2.75 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)OC[C@@H]1O[C@H](n2ccc(=O)[nH]c2=O)[C@@H](…`
ZINC5104175	0.688	287.2 Da LogP -2.75 TPSA 156.9	✓ Ro5	✓ Clean	`NC(=O)OC[C@@H]1O[C@@H](n2ccc(=O)[nH]c2=O)[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.