Protein target profile

VK055_1428

heme-containing peroxidase/deferrochelatase

Genome: KpATCC43816 Gene: AIK80049.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GMM5

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Length 427

Pocket druggability 0.976

Metabolic reactions 2

Chokepoint No

Direct ligand evidence 0 3 total records

Functional annotation 1 EC 8 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

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.98. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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: 2.2% 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: Periplasmic

Structure confidence

ColabFold pLDDT: 91.08 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 0.976

Structure A0A0H3GMM5

Pocket Pocket 4

P2Rank 0.977

Structure A0A0H3GMM5

Pocket Pocket 1

ColabFold model

FPocket 0.984 · Pocket 1

P2Rank 0.98 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 105 / 4744 genomes with a hit

Prevalence 2.2%

Cross-references

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

Sequence

UniProt A0A0H3GMM5

Pathways

BioCyc PROTOHEMEFERROCHELAT-RXN[CCO-CYTOSOL]-PROTOHEME/PROTON//PROTOPORPHYRIN_IX/FE+2.54. BioCyc PROTOHEMEFERROCHELAT-RXN[CCO-PERI-BAC]-PROTOHEME/PROTON//PROTOPORPHYRIN_IX/FE+2.55.

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome

Chokepoint Not a chokepoint

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MAQQKPHDVNEPSRRRLLKGIGALGGALAITGGCPVAHAAKAESSPGTLTPDARQEKQPFYGRHQAGILTPQQASMMLVAFDVLAADKADLERLFRLLTQRIAFLTQGGPAPDTPNPLLPPMDSGILGPWIAPDNLTITVSVGHSLFDERFGLADKAPKKLQPMTRFPNDSLDAALCHGDLLLQICANTQDTVIHALRDVIKHTPDLLSVRWKREGFISDSAARSKGKETPINLLGFKDGTANPASHDSALMDKVVWVTADQDEPAWTVGGSYQAARIIQFHVEFWDRTPLKEQQTIFGRDKHTGAPLGMKNEHDTPDYSKDPNGEVIALDSHIRLANPRTPETQSSLMMRRGYSYSLGVTNAGQLDMGLLFVCYQHDLEKGFLTVQKRLNGEALEEYVKPIGGGYFFVLPGVVDEKHYLGESLLQA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1.11.1.-

Gene Ontology (GO)

GO:0033212 The directed movement of iron ions from outside of a cell into the cytoplasmic compartment. This may occur via transport across the plasma membrane or via endocytosis.
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:0030313 An envelope that surrounds a bacterial cell and includes the cytoplasmic membrane and everything external, encompassing the periplasmic space, cell wall, and outer membrane if present.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0042597 The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
GO:0004325 Catalysis of the reaction: heme B (protoheme) + H+ = Fe(2+) + protoporphyrin IX.
GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

22 records

Show feature table

Start	End	DB	Term	Name
57	415	PANTHER	PTHR30521	DEFERROCHELATASE/PEROXIDASE
57	415	InterPro	IPR006314	Dyp-type peroxidase
65	413	NCBIfam	TIGR01413	Dyp-type peroxidase
65	413	InterPro	IPR006314	Dyp-type peroxidase
62	419	ProSiteProfiles	PS51404	DyP-type peroxidase family.
62	419	InterPro	IPR006314	Dyp-type peroxidase
1	34	ProSiteProfiles	PS51257	Prokaryotic membrane lipoprotein lipid attachment site profile.
1	39	SignalP_GRAM_POSITIVE	SignalP-TM	SignalP-TM
65	413	Pfam	PF04261	Dyp-type peroxidase family
20	31	Phobius	SIGNAL_PEPTIDE_H_REGION	Hydrophobic region of a signal peptide.
1	19	Phobius	SIGNAL_PEPTIDE_N_REGION	N-terminal region of a signal peptide.
32	39	Phobius	SIGNAL_PEPTIDE_C_REGION	C-terminal region of a signal peptide.
13	39	NCBIfam	TIGR01409	twin-arginine translocation signal domain
13	39	InterPro	IPR019546	Twin-arginine translocation pathway, signal sequence, bacterial/archaeal
1	39	Phobius	SIGNAL_PEPTIDE	Signal peptide region
7	426	NCBIfam	TIGR01412	iron uptake transporter deferrochelatase/peroxidase subunit
7	426	InterPro	IPR006313	Deferrochelatase
1	39	ProSiteProfiles	PS51318	Twin arginine translocation (Tat) signal profile.
1	39	InterPro	IPR006311	Twin-arginine translocation pathway, signal sequence
40	427	Phobius	NON_CYTOPLASMIC_DOMAIN	Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
58	419	SUPERFAMILY	SSF54909	Dimeric alpha+beta barrel
58	419	InterPro	IPR011008	Dimeric alpha-beta barrel

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 #4

0.976

Likely same site as P2Rank 1 1.0 Å 31 shared residues 94% of smaller site

Unusual size

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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

0.977

Likely same site as FPocket 4 1.0 Å 31 shared residues 94% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.039

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Surrounding area

Residue sets

UniProt: Binding site:240-242

UniProt: Binding site:300-300

UniProt: Binding site:333-333

UniProt: Binding site:338-340

UniProt: Binding site:351-351

Binding pockets · P2Rank

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

Site 1 P2Rank #1

0.98

Likely same site as FPocket 1 1.5 Å 35 shared residues 92% of smaller site

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Surrounding area

Site 2 P2Rank #2

0.18

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Surrounding area

Site 3 P2Rank #3

0.037

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Surrounding area

Residue sets

UniProt: Binding site:240-242

UniProt: Binding site:300-300

UniProt: Binding site:333-333

UniProt: Binding site:338-340

UniProt: Binding site:351-351

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_A0A0H3GMM5	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_1428	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.

3 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 3 records from similar proteins

Structural ligands 3 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 0 similarity-based ZINC candidates

Best available ligand signal

OXY PDB via homolog 32.0 Da · LogP 0.07 · TPSA 34.1 Open detail RCSB PDB

PEO PDB via homolog Detail RCSB PDB

PP9 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.

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
OXY RCSB PDB	6JBN	A0A6I8WFL8	32.0 Da LogP 0.07 TPSA 34.1	✓ Ro5	✓ Clean	`O=O`
PEO RCSB PDB	4GRC	Q9RKQ2	34.0 Da LogP 0.02 TPSA 40.5	✓ Ro5	✓ Clean	`OO`
PP9 RCSB PDB	2Y4E	P31545	562.7 Da LogP 7.50 TPSA 132.0	2 viol.	✓ Clean	`Cc1c2\cc\3/nc(\cc/4\c(c(/c(/[nH]4)c/c5n/c(c\c(c…`

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.