Protein profile

VK055_4163

peptide chain release factor 2

Genome: KpATCC43816

Gene: AIK82709.1 prfB Structure source: AlphaFold + ColabFold UniProt A0A0H3GSW3

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Amino acids 293

Annotations 4

Features 21

PDB binders 1

Druggability 0.048

Overview

Basic information about this protein and its source genome.

Accession: VK055_4163
Assembly: Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene: AIK82709.1 prfB
Status: annotated
Amino acids: 293
Structure source: AlphaFold + ColabFold

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0006415 The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code). GO:0003747 Involved in catalyzing the release of a nascent polypeptide chain from a ribosome. GO:0016149 A translation release factor that is specific for one or more particular termination codons; acts at the ribosomal A-site and require polypeptidyl-tRNA at the P-site.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 49.206
Human E-value: 3.63e-36
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 96.928
DEG E-value: 0.0
Localization: Cytoplasmic
ColabFold pLDDT: 89.36

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 0.048

Structure A0A0H3GSW3

Pocket Pocket 14

P2Rank 0.014

Structure A0A0H3GSW3

Pocket Pocket 1

ColabFold model

FPocket 0.015 · Pocket 21

P2Rank 0.007 · Pocket 1

Core conservation Accessory gene

Roary core

CoreCruncher accessory

Gut microbiome 2049 / 4744 genomes with a hit

Normalized 0.432

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
GO:0006415 The process resulting in the release of a polypeptide chain from the ribosome, usually in response to a termination codon (UAA, UAG, or UGA in the universal genetic code).
GO:0003747 Involved in catalyzing the release of a nascent polypeptide chain from a ribosome.
GO:0016149 A translation release factor that is specific for one or more particular termination codons; acts at the ribosomal A-site and require polypeptidyl-tRNA at the P-site.

Sequence Features

Domain/signature hits from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
58	286	Gene3D	G3DSA:3.30.70.1660	-
2	292	SUPERFAMILY	SSF75620	Release factor
2	292	InterPro	IPR045853	Peptide chain release factor class I superfamily
2	290	NCBIfam	TIGR00020	peptide chain release factor 2
2	290	InterPro	IPR004374	Peptide chain release factor 2
154	249	Gene3D	G3DSA:3.30.160.20	-
173	189	ProSitePatterns	PS00745	Prokaryotic-type class I peptide chain release factors signature.
173	189	InterPro	IPR000352	Peptide chain release factor class I
13	123	SMART	SM00937	PCRF_a_2
13	123	InterPro	IPR005139	Peptide chain release factor
17	44	Coils	Coil	Coil
7	147	Pfam	PF03462	PCRF domain
7	147	InterPro	IPR005139	Peptide chain release factor
1	44	Gene3D	G3DSA:1.20.58.410	Release factor
1	293	Hamap	MF_00094	Peptide chain release factor 2 [prfB].
1	293	InterPro	IPR004374	Peptide chain release factor 2
154	249	FunFam	G3DSA:3.30.160.20:FF:000010	Peptide chain release factor 2
3	290	PANTHER	PTHR43116	PEPTIDE CHAIN RELEASE FACTOR 2
216	241	Coils	Coil	Coil
156	265	Pfam	PF00472	RF-1 domain
156	265	InterPro	IPR000352	Peptide chain release factor class I

3D Structure

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

No pockets are loaded yet for the displayed AlphaFold model AF_A0A0H3GSW3 structure. Run experimental pocket backfill to show FPocket/P2Rank overlays on this structure.

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_A0A0H3GSW3	AlphaFold	—	—	full sequence	—	Viewing
ColabFold VK055_4163	ColabFold	—	—	full sequence	—	Loaded

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
FME	5MDV	P07012	177.2 Da LogP -0.06 TPSA 66.4	✓ Ro5	✓ Clean	`CSCC[C@@H](C(=O)O)NC=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
ZINC221146246	0.781	308.4 Da LogP 0.18 TPSA 95.5	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@H](CCSC)NC=O)C(=O)O`
ZINC4544549	0.758	439.6 Da LogP 0.41 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@H](CCSC)NC(=O)[C@H](CCSC)NC=…`
ZINC2116511	0.686	248.3 Da LogP -0.56 TPSA 95.5	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@@H](C)C(=O)O`
ZINC1576667	0.649	276.4 Da LogP 0.08 TPSA 95.5	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@H](C(=O)O)C(C)C`
ZINC4899576	0.625	335.4 Da LogP -2.08 TPSA 144.8	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@@H](C)C(=O)N[C@@H](CO)C…`
ZINC8076277	0.625	305.4 Da LogP -0.45 TPSA 121.5	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@@H](CCCCN)C(=O)O`
ZINC5759645	0.610	361.5 Da LogP -0.03 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@@H](C)C(=O)N[C@@H](CC(C…`
ZINC1576194	0.595	324.4 Da LogP 0.67 TPSA 95.5	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@@H](Cc1ccccc1)NC=O)C(=O)O`
ZINC1576195	0.595	324.4 Da LogP 0.67 TPSA 95.5	✓ Ro5	✓ Clean	`CSCC[C@@H](NC(=O)[C@@H](Cc1ccccc1)NC=O)C(=O)O`
ZINC1576196	0.595	324.4 Da LogP 0.67 TPSA 95.5	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@H](Cc1ccccc1)NC=O)C(=O)O`
ZINC1576197	0.595	324.4 Da LogP 0.67 TPSA 95.5	✓ Ro5	✓ Clean	`CSCC[C@@H](NC(=O)[C@H](Cc1ccccc1)NC=O)C(=O)O`
ZINC2516173	0.595	324.4 Da LogP 0.67 TPSA 95.5	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@@H](Cc1ccccc1)C(=O)O`
ZINC13550236	0.581	419.5 Da LogP -0.18 TPSA 161.9	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H]…`
ZINC15721376	0.581	455.6 Da LogP 0.90 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@@H](CCSC)C(=O)N[C@@H](C…`
ZINC4544540	0.581	455.6 Da LogP 0.90 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@H](Cc1ccccc1)NC(=O)[C@H](CCS…`
ZINC5768212	0.576	205.3 Da LogP 0.72 TPSA 66.4	✓ Ro5	✓ Clean	`CCC(=O)N[C@@H](CCSC)C(=O)O`
ZINC5768215	0.576	205.3 Da LogP 0.72 TPSA 66.4	✓ Ro5	✓ Clean	`CCC(=O)N[C@H](CCSC)C(=O)O`
ZINC37965632	0.559	205.3 Da LogP 1.44 TPSA 49.3	✓ Ro5	✓ Clean	`CSCC[C@H](NCC(C)C)C(=O)O`
ZINC37965633	0.559	205.3 Da LogP 1.44 TPSA 49.3	✓ Ro5	✓ Clean	`CSCC[C@@H](NCC(C)C)C(=O)O`
ZINC2121521	0.550	287.3 Da LogP -0.97 TPSA 124.6	✓ Ro5	Alert	`CSCC[C@H](NC=C1C(=O)NC(=O)NC1=O)C(=O)O`
ZINC2121524	0.550	287.3 Da LogP -0.97 TPSA 124.6	✓ Ro5	Alert	`CSCC[C@@H](NC=C1C(=O)NC(=O)NC1=O)C(=O)O`
ZINC142128194	0.543	221.3 Da LogP -0.31 TPSA 86.6	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@H](C)O)C(=O)O`
ZINC1569422	0.543	206.3 Da LogP -0.73 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](NC(=O)CN)C(=O)O`
ZINC1569524	0.543	206.3 Da LogP -0.73 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)CN)C(=O)O`
ZINC1672830	0.543	221.3 Da LogP 0.26 TPSA 86.6	✓ Ro5	✓ Clean	`CSCC[C@H](NCCC(=O)O)C(=O)O`
ZINC214816170	0.543	221.3 Da LogP -0.31 TPSA 86.6	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@@H](C)O)C(=O)O`
ZINC214816217	0.543	221.3 Da LogP -0.31 TPSA 86.6	✓ Ro5	✓ Clean	`CSCC[C@@H](NC(=O)[C@H](C)O)C(=O)O`
ZINC3331958	0.543	241.3 Da LogP 0.13 TPSA 83.5	✓ Ro5	✓ Clean	`CCS(=O)(=O)N[C@@H](CCSC)C(=O)O`
ZINC3331960	0.543	241.3 Da LogP 0.13 TPSA 83.5	✓ Ro5	✓ Clean	`CCS(=O)(=O)N[C@H](CCSC)C(=O)O`
ZINC41689785	0.543	219.3 Da LogP 1.83 TPSA 49.3	✓ Ro5	✓ Clean	`CSCC[C@H](NCCC(C)C)C(=O)O`
ZINC41689788	0.543	219.3 Da LogP 1.83 TPSA 49.3	✓ Ro5	✓ Clean	`CSCC[C@@H](NCCC(C)C)C(=O)O`
ZINC8614599	0.543	221.3 Da LogP 0.26 TPSA 86.6	✓ Ro5	✓ Clean	`CSCC[C@@H](NCCC(=O)O)C(=O)O`
ZINC100716065	0.537	303.3 Da LogP 0.50 TPSA 101.9	✓ Ro5	Alert	`CSCC[C@H](NC=C1C(=O)OC(C)(C)OC1=O)C(=O)O`
ZINC100716069	0.537	303.3 Da LogP 0.50 TPSA 101.9	✓ Ro5	Alert	`CSCC[C@@H](NC=C1C(=O)OC(C)(C)OC1=O)C(=O)O`
ZINC3874395	0.532	437.6 Da LogP 1.20 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@@H](NC=O)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H…`
ZINC3874396	0.532	437.6 Da LogP 1.20 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@@H](NC=O)C(=O)N[C@H](CC(C)C)C(=O)N[C@@H]…`
ZINC3874397	0.532	437.6 Da LogP 1.20 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@@H](NC=O)C(=O)N[C@@H](CC(C)C)C(=O)N[C@H]…`
ZINC3874398	0.532	437.6 Da LogP 1.20 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@@H](NC=O)C(=O)N[C@H](CC(C)C)C(=O)N[C@H](…`
ZINC4099172	0.532	437.6 Da LogP 1.20 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@@H](CC(C)C)C(=O)N[C@@H]…`
ZINC9212385	0.532	437.6 Da LogP 1.20 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@@H](CC(C)C)C(=O)N[C@H](…`
ZINC9212386	0.532	437.6 Da LogP 1.20 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@H](CC(C)C)C(=O)N[C@H](C…`
ZINC9212387	0.532	437.6 Da LogP 1.20 TPSA 124.6	✓ Ro5	✓ Clean	`CSCC[C@H](NC=O)C(=O)N[C@H](CC(C)C)C(=O)N[C@@H](…`
ZINC1605258	0.528	280.4 Da LogP 0.39 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@H](N)CCSC)C(=O)O`
ZINC1605259	0.528	280.4 Da LogP 0.39 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](N)C(=O)N[C@H](CCSC)C(=O)O`
ZINC1605260	0.528	280.4 Da LogP 0.39 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](N)C(=O)N[C@H](CCSC)C(=O)O`
ZINC1692507	0.528	249.3 Da LogP 0.17 TPSA 103.7	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)CCC(=O)O)C(=O)O`
ZINC1708198	0.528	220.3 Da LogP -0.34 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)[C@@H](C)N)C(=O)O`
ZINC1708199	0.528	220.3 Da LogP -0.34 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](NC(=O)[C@H](C)N)C(=O)O`
ZINC1708200	0.528	220.3 Da LogP -0.34 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](NC(=O)[C@@H](C)N)C(=O)O`
ZINC2043758	0.528	249.3 Da LogP 0.17 TPSA 103.7	✓ Ro5	✓ Clean	`CSCC[C@@H](NC(=O)CCC(=O)O)C(=O)O`

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.