Protein target profile

KP13_03540

putative iron-dependent peroxidase

Genome: KpKP13 Gene: AHE43346.1 3D evidence: Experimental + ColabFold model UniProt A0A0W8ATM9

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Length 299

Pocket druggability 0.991

Direct ligand evidence 1 2 total records

Functional annotation 1 EC 4 GO

Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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

Main supporting evidence

Independent pocket support: FPocket + P2Rank Both predictors report a high-scoring binding site (FPocket 0.99, P2Rank 0.99). Use the 3D pocket comparison to verify whether they identify the same site. Experimental structure available At least one PDB experimental structure is loaded, not just a predicted model - stronger structural coverage than AlphaFold/ColabFold alone. Direct ligand evidence 1 direct ligand records. Strong known ligand: co-crystal structure 1 PDB record(s) show a ligand actually co-crystallized with this exact protein - real experimental evidence, not a computational prediction. Review the complete evidence below

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: No hit
Gut microbiome similarity: 2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): N
DEG identity (%): 0.0 Higher values support similarity to known essential genes.

Localization

Localization: Cytoplasmic

Structure confidence

ColabFold pLDDT: 97.57 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

PDB experimental structure

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 0.991

Structure 6FIY

Pocket Pocket 1

P2Rank 0.988

Structure 6FIY

Pocket Pocket 1

ColabFold model

FPocket 0.934 · Pocket 1

P2Rank 0.931 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 107 / 4744 genomes with a hit

Prevalence 2.3%

Cross-references

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

Sequence

UniProt A0A0W8ATM9

Structure

PDB 6FIY PDB 6FL2 PDB 6RPD PDB 6FKS PDB 6RPE PDB 6FKT PDB 6RQY PDB 6RR1 PDB 6RR4 PDB 6RR5 PDB 6RR6 PDB 6RR8

Sequence

Primary amino-acid sequence viewer.

MSQVQSGILPEHCRAAIWIEANLKGDVNALREASKIFVDNVATFQAKFPDAKLGAVVAFGNNVWRQLSGGEGADELKDFPVYGKGLAPSTQYDLLIHILSARHEVNFSVAQAALAAFGDAIDVKEEIHGFRWVEERDLSGFVDGTENPAGEETRREVAVIKDGVDAGGSYVFVQRWEHNLKQLNRMSVPDQEMMIGRTKDANEEIDGDERPVTSHLSRVDLKEDGKGLKIVRQSLPYGTASGTHGLYFCAYCARLYNIEQQLLSMFGDTDGKRDAMLRFTKPVTGGYYFAPSLERIQAL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1.11.1.-

Gene Ontology (GO)

GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
GO:0004601 Catalysis of the reaction: a reduced substrate + ROOH = an oxidized substrate + ROH + H2O.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

9 records

Show feature table

Start	End	DB	Term	Name
1	297	SUPERFAMILY	SSF54909	Dimeric alpha+beta barrel
1	297	InterPro	IPR011008	Dimeric alpha-beta barrel
5	294	Pfam	PF04261	Dyp-type peroxidase family
5	294	InterPro	IPR006314	Dyp-type peroxidase
5	294	NCBIfam	TIGR01413	Dyp-type peroxidase
2	299	ProSiteProfiles	PS51404	DyP-type peroxidase family.
2	299	InterPro	IPR006314	Dyp-type peroxidase
2	298	PANTHER	PTHR30521	DEFERROCHELATASE/PEROXIDASE
2	298	InterPro	IPR006314	Dyp-type peroxidase

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

0.991

Likely same site as P2Rank 1 1.4 Å 15 shared residues 75% of smaller site

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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

0.988

Likely same site as FPocket 1 1.4 Å 15 shared residues 75% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.016

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Surrounding area

Site 3 P2Rank #3

0.003

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Surrounding area

All structural evidence 12 experimental · 1 predicted

Structural evidence

12 + 1

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
PDB 6FIY	X-ray	1.09 Å	A,B	100.0% 1-299	PDBe RCSB PDBj File	Viewing
PDB 6FL2	X-ray	1.27 Å	A,B	100.0% 1-299	PDBe RCSB PDBj File	Loaded
PDB 6RPD	X-ray	1.52 Å	A,B	100.0% 1-299	PDBe RCSB PDBj File	Loaded
PDB 6FKS	X-ray	1.60 Å	A,B	100.0% 1-299	PDBe RCSB PDBj File	Loaded
PDB 6RPE	X-ray	1.80 Å	A,B	100.0% 1-299	PDBe RCSB PDBj File	Loaded
PDB 6FKT	X-ray	1.86 Å	A,B	100.0% 1-299	PDBe RCSB PDBj File	Loaded
PDB 6RQY	X-ray	1.90 Å	A,B	100.0% 1-299	PDBe RCSB PDBj File	Loaded
PDB 6RR1	X-ray	1.90 Å	A,B	100.0% 1-299	PDBe RCSB PDBj File	Loaded
PDB 6RR4	X-ray	1.90 Å	A,B	100.0% 1-299	PDBe RCSB PDBj File	Loaded
PDB 6RR5	X-ray	1.90 Å	A,B	100.0% 1-299	PDBe RCSB PDBj File	Loaded
PDB 6RR6	X-ray	1.90 Å	A,B	100.0% 1-299	PDBe RCSB PDBj File	Loaded
PDB 6RR8	X-ray	1.90 Å	A,B	100.0% 1-299	PDBe RCSB PDBj File	Loaded
ColabFold KP13_03540	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.

2 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 1 same-protein records

Transferred evidence 1 records from similar proteins

Structural ligands 2 1 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 0 similarity-based ZINC candidates

Best available ligand signal

NO2 PDB co-crystal 46.0 Da · LogP 0.25 · TPSA 52.5 Open detail RCSB PDB

OXY PDB via homolog Detail RCSB PDB

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.

Ligand	Source crystal	MW · LogP · TPSA	Lipinski	PAINS	SMILES
NO2 RCSB PDB	6FL2 1.27 Å Open crystal	46.0 Da LogP 0.25 TPSA 52.5	✓ Ro5	✓ Clean	`N(=O)[O-]`

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
OXY RCSB PDB	6JBN	A0A6I8WFL8	32.0 Da LogP 0.07 TPSA 34.1	✓ Ro5	✓ Clean	`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).

No virtual-screening candidates for this protein.

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.