Protein target profile

KP13_02198

Peptide chain release factor 2

Genome: KpKP13 Gene: prfB AHE42767.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GSW3

Export view

Length 320

Pocket druggability 0.048

Direct ligand evidence 0 51 total records

Functional annotation 0 EC 4 GO

Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target: Hit
Human identity (%): 49.206 Lower values reduce human off-target concern.
Human E-value: 7.54e-36
Gut microbiome similarity: 18.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 96.562 Higher values support similarity to known essential genes.
DEG E-value: 0.0 Smaller values mean stronger essential-gene similarity.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 88.64 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.048

Structure A0A0H3GSW3

Pocket Pocket 14

P2Rank 0.014

Structure A0A0H3GSW3

Pocket Pocket 1

ColabFold model

FPocket 0.778 · Pocket 24

P2Rank 0.01 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 889 / 4744 genomes with a hit

Prevalence 18.7%

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GSW3

Sequence

Primary amino-acid sequence viewer.

MWNEPERAQALGKERSSLEAIVDTLDQMSQGLEDVAGLLDLAVEADDEETFNEAVAELDTLEEKLAQLEFRRMFSGEYDSADCYLDIQAGSGGTEAQDWASMLMRMYLRWAEARGFKTEIIEESEGEVAGIKSVTIKIIGDYAYGWLRTETGVHRLVRKSPFDSGGRRHTSFSSAFVYPEVEDDIDIEINPADLRIDVYRASGAGGQHVNRTESAVRITHIPTGLVTQCQNDRSQHKNKDQAMKQMKAKLYELEMQKKNAEKQAMEDNKSDIGWGSQIRSYVLDDSRIKDLRTGVETRNTQAVLDGSLDQFIEASLKAGL

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:0003747 Involved in catalyzing the release of a nascent polypeptide chain from a ribosome.
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: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 domains and features

Domain and signature matches imported from InterPro and related databases.

21 records

Show feature table

Start	End	DB	Term	Name
183	292	Pfam	PF00472	RF-1 domain
183	292	InterPro	IPR000352	Peptide chain release factor class I
2	319	SUPERFAMILY	SSF75620	Release factor
2	319	InterPro	IPR045853	Peptide chain release factor class I superfamily
200	216	ProSitePatterns	PS00745	Prokaryotic-type class I peptide chain release factors signature.
200	216	InterPro	IPR000352	Peptide chain release factor class I
44	71	Coils	Coil	Coil
1	174	Pfam	PF03462	PCRF domain
1	174	InterPro	IPR005139	Peptide chain release factor
1	317	NCBIfam	TIGR00020	peptide chain release factor 2
1	317	InterPro	IPR004374	Peptide chain release factor 2
85	313	Gene3D	G3DSA:3.30.70.1660	-
243	268	Coils	Coil	Coil
40	150	SMART	SM00937	PCRF_a_2
40	150	InterPro	IPR005139	Peptide chain release factor
181	276	Gene3D	G3DSA:3.30.160.20	-
1	71	Gene3D	G3DSA:1.20.58.410	Release factor
1	317	PANTHER	PTHR43116	PEPTIDE CHAIN RELEASE FACTOR 2
1	320	Hamap	MF_00094	Peptide chain release factor 2 [prfB].
1	320	InterPro	IPR004374	Peptide chain release factor 2
181	276	FunFam	G3DSA:3.30.160.20:FF:000010	Peptide chain release factor 2

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

Download VMD script Full viewer

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

Pocket score High Medium Low

How colors and pocket overlays are used

Uniform protein color marks the displayed model as a single molecular object.

Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.

Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.

'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.

'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.

'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.

Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1

0.014

Show in viewer

Surrounding area

Site 2 P2Rank #2

0.008

Show in viewer

Surrounding area

All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold DB AF_A0A0H3GSW3	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_02198	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

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 1 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

FME PDB via homolog 177.2 Da · LogP -0.06 · TPSA 66.4 Open detail RCSB PDB

ZINC221146246 ZINC proposed compound · Tanimoto 0.781 Detail ZINC

ZINC4544549 ZINC proposed compound · Tanimoto 0.758 Detail ZINC

ZINC2116511 ZINC proposed compound · Tanimoto 0.686 Detail ZINC

ZINC1576667 ZINC proposed compound · Tanimoto 0.649 Detail ZINC

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, 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 RCSB PDB	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	0.576	205.3 Da LogP 0.72 TPSA 66.4	✓ Ro5	✓ Clean	`CCC(=O)N[C@@H](CCSC)C(=O)O`
ZINC5768215 ZINC	0.576	205.3 Da LogP 0.72 TPSA 66.4	✓ Ro5	✓ Clean	`CCC(=O)N[C@H](CCSC)C(=O)O`
ZINC37965632 ZINC	0.559	205.3 Da LogP 1.44 TPSA 49.3	✓ Ro5	✓ Clean	`CSCC[C@H](NCC(C)C)C(=O)O`
ZINC37965633 ZINC	0.559	205.3 Da LogP 1.44 TPSA 49.3	✓ Ro5	✓ Clean	`CSCC[C@@H](NCC(C)C)C(=O)O`
ZINC2121521 ZINC	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 ZINC	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 ZINC	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 ZINC	0.543	206.3 Da LogP -0.73 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@@H](NC(=O)CN)C(=O)O`
ZINC1569524 ZINC	0.543	206.3 Da LogP -0.73 TPSA 92.4	✓ Ro5	✓ Clean	`CSCC[C@H](NC(=O)CN)C(=O)O`
ZINC1672830 ZINC	0.543	221.3 Da LogP 0.26 TPSA 86.6	✓ Ro5	✓ Clean	`CSCC[C@H](NCCC(=O)O)C(=O)O`
ZINC214816170 ZINC	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 ZINC	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 ZINC	0.543	241.3 Da LogP 0.13 TPSA 83.5	✓ Ro5	✓ Clean	`CCS(=O)(=O)N[C@@H](CCSC)C(=O)O`
ZINC3331960 ZINC	0.543	241.3 Da LogP 0.13 TPSA 83.5	✓ Ro5	✓ Clean	`CCS(=O)(=O)N[C@H](CCSC)C(=O)O`
ZINC41689785 ZINC	0.543	219.3 Da LogP 1.83 TPSA 49.3	✓ Ro5	✓ Clean	`CSCC[C@H](NCCC(C)C)C(=O)O`
ZINC41689788 ZINC	0.543	219.3 Da LogP 1.83 TPSA 49.3	✓ Ro5	✓ Clean	`CSCC[C@@H](NCCC(C)C)C(=O)O`
ZINC8614599 ZINC	0.543	221.3 Da LogP 0.26 TPSA 86.6	✓ Ro5	✓ Clean	`CSCC[C@@H](NCCC(=O)O)C(=O)O`
ZINC100716065 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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 ZINC	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.

KP13_02198

Target candidate with partial support; inspect missing evidence before prioritizing.

Main supporting evidence

Risks to review

Evidence gaps

Prioritization evidence

Off-target risk

Essentiality

Localization

Structure confidence

Binding-site evidence

Cross-references

Sequence

Sequence

Functional annotations

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · P2Rank

Binding pockets · FPocket

Binding pockets · P2Rank

Structural evidence

Ligand evidence