KpATCC43816 Protein target profile

ferrochelatase

Accession: VK055_2092

Gene: AIK80697.1 hemH 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GNR2
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Length 320
Pocket druggability (P2Rank · AlphaFold DB model) 0.967
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 62 total records
Functional annotation 1 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. Second pocket predictor agrees P2Rank predicted binding-site probability 0.97. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 9 structural and 3 bioactivity records.

Risks to review

Human similarity Top human hit identity: 33.333%. This target also has a predicted binding pocket (P2Rank 0.97) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 149 of 4744 screened genomes (3.1%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.97) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.91, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity.

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
Hit
Human identity (%)
33.333 Lower values reduce human off-target concern.
Human E-value
4.48e-14
Gut microbiome similarity
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
97.09 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank) 0.967
Structure A0A0H3GNR2
Pocket Pocket 1
Druggability (FPocket) 0.914
Structure A0A0H3GNR2
Pocket Pocket 12
ColabFold model
P2Rank 0.974 · Pocket 1
FPocket 0.774 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 149 / 4744 genomes with a hit
Prevalence 3.1%

Metabolic context

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

Explore metabolic network
Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

2 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MHQTKTGILLANLGTPDAPTPGAVKRYLRQFLSDKRVVDTSRLLWWPLLRGVILPIRSPRVAKLYQSVWMEEGSPLMVYSRRQQQALAARLPDTPVALGMSYGSPSLASAVDDLLAQGVEHIVVLPLYPQYSCSTVAAVWDELARILAKKRAIPGISFIRDYAEHPDYIHALAASVRASFAVHGEPDLLLLSYHGIPQRYANQGDDYPQRCRDTTRELVSALGLPPERVMMTFQSRFGREPWLTPYTDETLKMLGEKGTKHIQVLCPGFAADCLETLEEIAVQNREIFLEAGGKQYEYIPALNADAAHIEMMVNLTAPYR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0004325 Catalysis of the reaction: heme B (protoheme) + H+ = Fe(2+) + protoporphyrin IX.
  • GO:0006783 The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, from less complex precursors.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0046872 Binding to a metal ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
170 303 CDD cd00419 Ferrochelatase_C
170 303 InterPro IPR033644 Ferrochelatase, C-terminal
4 320 Hamap MF_00323 Coproporphyrin III ferrochelatase [cpfC].
4 320 InterPro IPR001015 Ferrochelatase
5 316 Gene3D G3DSA:3.40.50.1400 -
5 177 FunFam G3DSA:3.40.50.1400:FF:000004 Ferrochelatase
2 316 NCBIfam TIGR00109 ferrochelatase
2 316 InterPro IPR001015 Ferrochelatase
163 301 Gene3D G3DSA:3.40.50.1400 -
5 316 Pfam PF00762 Ferrochelatase
5 316 InterPro IPR001015 Ferrochelatase
6 165 CDD cd03411 Ferrochelatase_N
6 165 InterPro IPR033659 Ferrochelatase, N-terminal
189 207 ProSitePatterns PS00534 Ferrochelatase signature.
189 207 InterPro IPR019772 Ferrochelatase, active site
4 317 SUPERFAMILY SSF53800 Chelatase
3 315 PANTHER PTHR11108 FERROCHELATASE
3 315 InterPro IPR001015 Ferrochelatase

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

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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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.967
Likely same site as FPocket 12 0.7 Å 41 shared residues 95% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #12
0.914 Unusual size
Likely same site as P2Rank 1 0.7 Å 41 shared residues 95% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:194-194
UniProt: Binding site:275-275
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_A0A0H3GNR2
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_2092
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.

62 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 12 records from similar proteins
Structural ligands 9 0 loaded crystals
Measured bioactivity 3 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
CHD PDB via homolog 408.6 Da · LogP 3.45 · TPSA 98.0 Open detail RCSB PDB
FEC PDB via homolog Detail RCSB PDB
FES PDB via homolog Detail RCSB PDB
H01 PDB via homolog Detail RCSB PDB
H02 PDB via homolog Detail RCSB PDB

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.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
CHD RCSB PDB
7L78
P16622 408.6 Da LogP 3.45 TPSA 98.0 ✓ Ro5 ✓ Clean C[C@H](CCC(=O)O)[C@H]1CC[C@@H]2[C@@]1([C@H](C[C…
FEC RCSB PDB
6SV3
Q8Y565 708.5 Da LogP 2.75 TPSA 165.1 1 viol. ✓ Clean Cc1c2cc3[n+]4c(cc5c(c(c6n5[Fe@]47n2c(c1CCC(=O)O…
FES RCSB PDB
1HRK
P22830 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
H01 RCSB PDB
2Q2N
P32396 672.7 Da LogP 0.39 TPSA 246.5 2 viol. ✓ Clean Cc1c\2[nH]c(c1CCC(=O)O)\C=C/3\C(=C(/C(=C/c4c(c(…
H02 RCSB PDB
2Q3J
P32396 582.7 Da LogP 3.03 TPSA 126.9 1 viol. ✓ Clean CCc1c(c\2[nH]c1C=C3C(=C(C(=Cc4c(c(c([nH]4)C=C5C…
MMP RCSB PDB
1C1H
P32396 580.7 Da LogP 7.66 TPSA 121.1 2 viol. ✓ Clean CCc1c(c2cc3nc(\cc/4\c(c(/c(/[nH]4)c/c5n/c(c\c1n…
OXY RCSB PDB
3HCR
P22830 32.0 Da LogP 0.07 TPSA 34.1 ✓ Ro5 ✓ Clean O=O
PP9 RCSB PDB
2HRE
P22830 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…
SAL RCSB PDB
3W1W
P22830 138.1 Da LogP 1.09 TPSA 57.5 ✓ Ro5 ✓ Clean c1ccc(c(c1)C(=O)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.

Cross-references

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

Sequence

UniProt A0A0H3GNR2

Chemistry

ChEMBL CHEMBL1944698 ChEMBL CHEMBL482967 ChEMBL CHEMBL511692

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.