Protein profile

VK055_2906

oligoribonuclease monomer

Genome: KpATCC43816

Gene: yjeR AIK81492.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GQI6

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Amino acids 181

Annotations 5

Features 15

PDB binders 3

Druggability 0.317

Overview

Basic information about this protein and its source genome.

Accession: VK055_2906
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: yjeR AIK81492.1
Status: annotated
Amino acids: 181
Structure source: AlphaFold + ColabFold

3.1.-.-

GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule. GO:0003676 Binding to a nucleic acid. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0006259 Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 60.0
Human E-value: 4.57e-12
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 94.475
DEG E-value: 7.76e-129
Localization: Cytoplasmic
ColabFold pLDDT: 97.08

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 0.317

Structure A0A0H3GQI6

Pocket Pocket 8

P2Rank 0.712

Structure A0A0H3GQI6

Pocket Pocket 1

ColabFold model

FPocket 0.114 · Pocket 2

P2Rank 0.424 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 267 / 4744 genomes with a hit

Normalized 0.056

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

3.1.-.-

Gene Ontology (GO)

GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
GO:0003676 Binding to a nucleic acid.
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0006259 Any cellular metabolic process involving deoxyribonucleic acid. This is one of the two main types of nucleic acid, consisting of a long, unbranched macromolecule formed from one, or more commonly, two, strands of linked deoxyribonucleotides.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records

Show feature table

Start	End	DB	Term	Name
1	181	Gene3D	G3DSA:3.30.420.10	-
1	181	InterPro	IPR036397	Ribonuclease H superfamily
3	180	SUPERFAMILY	SSF53098	Ribonuclease H-like
3	180	InterPro	IPR012337	Ribonuclease H-like superfamily
8	179	CDD	cd06135	Orn
8	179	InterPro	IPR022894	Oligoribonuclease
53	174	PANTHER	PTHR11046	OLIGORIBONUCLEASE, MITOCHONDRIAL
53	174	InterPro	IPR022894	Oligoribonuclease
7	180	SMART	SM00479	exoiiiendus
7	180	InterPro	IPR013520	Exonuclease, RNase T/DNA polymerase III
1	181	FunFam	G3DSA:3.30.420.10:FF:000003	Oligoribonuclease
3	181	Hamap	MF_00045	Oligoribonuclease [orn].
3	181	InterPro	IPR022894	Oligoribonuclease
9	170	Pfam	PF00929	Exonuclease
9	170	InterPro	IPR013520	Exonuclease, RNase T/DNA polymerase III

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_A0A0H3GQI6	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_2906	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
8				0.317
5				0.232

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				9.86	0.53

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				5.46	0.26

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.

53 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
9RC	6A4D	Q47VZ4	443.3 Da LogP 0.60 TPSA 183.2	✓ Ro5	✓ Clean	`CC1=CN(C(=O)NC1=O)[C@H]2C[C@@H]([C@H](O2)COP(=O…`
FLC	1YTA	P0A784	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
MLI	6N6I	Q9Y3B8	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).

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
ZINC13520531	1.000	443.3 Da LogP 0.60 TPSA 183.2	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P@](=O)(O)Oc3ccc…`
ZINC13520567	0.746	443.3 Da LogP 0.60 TPSA 183.2	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O[P@](=O)(O)Oc3ccc([N+](=O)[…`
ZINC1532902	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O`
ZINC2018106	0.700	206.2 Da LogP -0.86 TPSA 132.1	✓ Ro5	✓ Clean	`O=C(O)CC[C@](O)(CC(=O)O)C(=O)O`
ZINC12503053	0.694	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=…`
ZINC33979243	0.694	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC33979244	0.694	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)OP(=O)…`
ZINC33979245	0.694	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=…`
ZINC33979246	0.694	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)OP(=O…`
ZINC8215882	0.694	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(O)OP(=O…`
ZINC13523519	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(=O)(O)O)O2)c(…`
ZINC1532628	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=…`
ZINC1678872	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=O…`
ZINC2047010	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870253	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O…`
ZINC3870254	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](COP(=O)(O)O)O2)c(=O)…`
ZINC6523446	0.683	322.2 Da LogP -1.40 TPSA 151.1	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(=O)(O)O)O2)c(=…`
ZINC13507072	0.672	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(O)O[P@…`
ZINC33979251	0.672	482.2 Da LogP -1.16 TPSA 244.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC3593496	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC3593497	0.652	206.2 Da LogP -1.16 TPSA 121.1	✓ Ro5	✓ Clean	`COC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC17107637	0.635	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@@H](COP(N)(N)=O)O2)c(…`
ZINC17107641	0.635	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](COP(N)(N)=O)O2)c(=…`
ZINC5493427	0.635	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](COP(N)(N)=O)O2)c(=O…`
ZINC5493430	0.635	320.2 Da LogP -1.46 TPSA 162.7	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](COP(N)(N)=O)O2)c(=…`
ZINC14686440	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…`
ZINC14686442	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…`
ZINC14686444	0.625	436.4 Da LogP -2.64 TPSA 247.9	1 viol.	✓ Clean	`O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…`
ZINC102804760	0.592	485.8 Da LogP 2.28 TPSA 152.9	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@](=O)(OCCC#N)O…`
ZINC102804763	0.592	485.8 Da LogP 2.28 TPSA 152.9	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO[P@](=O)(OCCC#N)…`
ZINC12654378	0.592	485.8 Da LogP 2.28 TPSA 152.9	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@@H](CO[P@@](=O)(OCCC#N…`
ZINC12654381	0.592	485.8 Da LogP 2.28 TPSA 152.9	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P@@](=O)(OCCC#N)…`
ZINC217356494	0.592	485.8 Da LogP 2.28 TPSA 152.9	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@@H](CO[P@](=O)(OCCC#N)O…`
ZINC35877795	0.592	485.8 Da LogP 2.28 TPSA 152.9	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@@H](O)[C@H](CO[P@@](=O)(OCCC#N)…`
ZINC8740033	0.592	485.8 Da LogP 2.28 TPSA 152.9	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(OCCC#N)…`
ZINC8740034	0.592	485.8 Da LogP 2.28 TPSA 152.9	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](O)[C@H](CO[P@@](=O)(OCCC#N)O…`
ZINC8740035	0.592	485.8 Da LogP 2.28 TPSA 152.9	✓ Ro5	✓ Clean	`Cc1cn([C@@H]2C[C@@H](O)[C@H](CO[P@@](=O)(OCCC#N…`
ZINC6667024	0.581	256.3 Da LogP -0.86 TPSA 93.5	✓ Ro5	✓ Clean	`COC[C@H]1O[C@@H](n2cc(C)c(=O)[nH]c2=O)C[C@@H]1O`
ZINC13398039	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O`
ZINC2528012	0.577	234.2 Da LogP -0.38 TPSA 121.1	✓ Ro5	✓ Clean	`CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O`
ZINC111459735	0.571	481.2 Da LogP -1.20 TPSA 249.9	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](N)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC138164075	0.571	498.2 Da LogP 0.21 TPSA 227.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`
ZINC11422512	0.567	402.2 Da LogP -1.28 TPSA 197.6	✓ Ro5	✓ Clean	`Cc1cn([C@H]2C[C@H](OP(=O)(O)O)[C@@H](COP(=O)(O)…`
ZINC146315135	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@@](O)(CC(=O)O)C(=O)O`
ZINC146315336	0.560	204.2 Da LogP 0.86 TPSA 94.8	✓ Ro5	✓ Clean	`CCCCC[C@](O)(CC(=O)O)C(=O)O`
ZINC1501317975	0.560	462.7 Da LogP 1.00 TPSA 174.5	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@H]([C@H]2C[C@H](O)[C@@H](CO[P@](=O…`
ZINC1501317976	0.560	462.7 Da LogP 1.00 TPSA 174.5	✓ Ro5	✓ Clean	`O=C1NC(=O)[C@@H]([C@H]2C[C@H](O)[C@@H](CO[P@](=…`
ZINC1695694	0.559	396.4 Da LogP 0.21 TPSA 127.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@H]2O[C@H](n3cc(C)c(=O)[nH]…`
ZINC4611593	0.559	396.4 Da LogP 0.21 TPSA 127.7	✓ Ro5	✓ Clean	`Cc1ccc(S(=O)(=O)OC[C@H]2O[C@@H](n3cc(C)c(=O)[nH…`
ZINC142512519	0.557	498.2 Da LogP 0.21 TPSA 227.1	2 viol.	✓ Clean	`Cc1cn([C@@H]2C[C@H](O)[C@H](CO[P@@](=O)(O)O[P@@…`

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.