Protein target profile

KP13_01463

Peptide chain release factor 1

Genome: KpKP13 Gene: prfA AHE44003.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GV19

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Length 360

Pocket druggability 0.771

Direct ligand evidence 0 51 total records

Functional annotation 0 EC 4 GO

Target summary

Promising target candidate with multiple supporting evidence streams.

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

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.77. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 1 structural and 0 bioactivity records.

Risks to review

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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 (%): 61.475 Lower values reduce human off-target concern.
Human E-value: 3.41e-45
Gut microbiome similarity: 40.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 92.778 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: 88.6 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 0.771

Structure A0A0H3GV19

Pocket Pocket 1

P2Rank 0.13

Structure A0A0H3GV19

Pocket Pocket 1

ColabFold model

FPocket 0.513 · Pocket 7

P2Rank 0.17 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 1922 / 4744 genomes with a hit

Prevalence 40.5%

Cross-references

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

Sequence

UniProt A0A0H3GV19

Sequence

Primary amino-acid sequence viewer.

MKSSIVAKLEALYERHEEVQALLGDAATIADQDKFRALSREYAQLSDVARCYTDWRQVQEDIETAQMMLDDPEMREMAQEELRDAKEKGDQLEQQLQVLLLPKDPDDERNAFVEVRAGTGGDEAALFAGDLFRMYTRYAESRRWQVEILSANEGEHGGFKEVIAKISGDGVYGRLKFESGGHRVQRVPATESQGRIHTSACTVAVMPELPEAEMPDINPADLRIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKALSVLGARIRAAEVAKRQQAEASTRRNLLGSGDRSDRNRTYNFPQGRVTDHRINLTLYRLDEAMEGKLDMLIEPIVQEHQADQLAALSEQE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

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.
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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records

Show feature table

Start	End	DB	Term	Name
5	357	Hamap	MF_00093	Peptide chain release factor 1 [prfA].
5	357	InterPro	IPR004373	Peptide chain release factor 1
211	305	FunFam	G3DSA:3.30.160.20:FF:000004	Peptide chain release factor 1
216	321	Pfam	PF00472	RF-1 domain
216	321	InterPro	IPR000352	Peptide chain release factor class I
223	282	Gene3D	G3DSA:3.30.160.20	-
1	358	NCBIfam	TIGR00019	peptide chain release factor 1
1	358	InterPro	IPR004373	Peptide chain release factor 1
278	360	FunFam	G3DSA:3.30.70.1660:FF:000004	Peptide chain release factor 1
107	218	FunFam	G3DSA:3.30.70.1660:FF:000002	Peptide chain release factor 1
14	203	Pfam	PF03462	PCRF domain
14	203	InterPro	IPR005139	Peptide chain release factor
12	353	SUPERFAMILY	SSF75620	Release factor
12	353	InterPro	IPR045853	Peptide chain release factor class I superfamily
290	314	MobiDBLite	mobidb-lite	consensus disorder prediction
107	222	Gene3D	G3DSA:3.30.70.1660	-
4	351	PANTHER	PTHR43804	LD18447P
286	314	MobiDBLite	mobidb-lite	consensus disorder prediction
75	95	Coils	Coil	Coil
1	106	Gene3D	G3DSA:6.10.140.1950	-
228	244	ProSitePatterns	PS00745	Prokaryotic-type class I peptide chain release factors signature.
228	244	InterPro	IPR000352	Peptide chain release factor class I
283	360	Gene3D	G3DSA:3.30.70.1660	-
63	178	SMART	SM00937	PCRF_a_2
63	178	InterPro	IPR005139	Peptide chain release factor

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.

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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 · FPocket

Druggability: high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Site 1 FPocket #1

0.771

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Surrounding area

Site 2 FPocket #10

0.315

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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.13

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Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.17

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Surrounding area

Site 2 P2Rank #2

0.022

Likely same site as FPocket 7 0.8 Å 7 shared residues 100% of smaller site

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Surrounding area

Site 3 P2Rank #3

0.005

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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_A0A0H3GV19	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold KP13_01463	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.