Protein target profile

KP13_03535

Coproporphyrinogen-III oxidase, aerobic

Genome: KpKP13 Gene: AHE43341.1 hemF 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVY6
Length 299
Pocket druggability 0.943
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 6 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.

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 (%)
60.0 Lower values reduce human off-target concern.
Human E-value
4.92e-11
Gut microbiome similarity
3.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
73.579 Higher values support similarity to known essential genes.
DEG E-value
1.91e-163 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
96.39 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 0.943
Structure A0A0H3GVY6
Pocket Pocket 23
P2Rank 0.986
Structure A0A0H3GVY6
Pocket Pocket 1
ColabFold model
FPocket 0.553 · Pocket 20
P2Rank 0.987 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 165 / 4744 genomes with a hit
Prevalence 3.5%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MKPDAAQVKTFLLQLQDSLCQQLSAVDGAPFIEDAWQREGGGGGRSRVLREGRVFEQAGVNFSHVHGDAMPASATAHRPELAGRSFEAMGVSLVVHPLNPYVPTSHANVRFFIAEKPGADPVWWFGGGFDLTPYYGFEEDAVHWHRTARDLCLPFGEEVYPRYKKWCDDYFYLKHRQEQRGIGGLFFDDLNTPDFDHCFAFMQAVGNGYADAYLPIVERRKATPYGERERHFQLYRRGRYVEFNLVWDRGTLFGLQTGGRTESILMSMPPLVRWEYDYQPEPGSPEAALSEFIQVRDWL

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0006779 The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
  • GO:0004109 Catalysis of the reaction: coproporphyrinogen III + 2 H+ + O2 = 2 CO2 + 2 H2O + protoporphyrinogen IX.
  • 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.
  • GO:0042803 Binding to an identical protein to form a homodimer.
  • GO:0006782 The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
1 299 PIRSF PIRSF000166 Coproporphyri_ox
1 299 InterPro IPR001260 Coproporphyrinogen III oxidase, aerobic
1 299 Gene3D G3DSA:3.40.1500.10 Coproporphyrinogen III oxidase, aerobic
1 299 InterPro IPR036406 Oxygen-dependent coproporphyrinogen III oxidase superfamily
164 188 ProSitePatterns PS01021 Coproporphyrinogen III oxidase signature.
164 188 InterPro IPR018375 Coproporphyrinogen III oxidase, conserved site
5 299 PANTHER PTHR10755 COPROPORPHYRINOGEN III OXIDASE, MITOCHONDRIAL
5 299 InterPro IPR001260 Coproporphyrinogen III oxidase, aerobic
123 145 PRINTS PR00073 Coprogen oxidase signature
123 145 InterPro IPR001260 Coproporphyrinogen III oxidase, aerobic
46 67 PRINTS PR00073 Coprogen oxidase signature
46 67 InterPro IPR001260 Coproporphyrinogen III oxidase, aerobic
88 112 PRINTS PR00073 Coprogen oxidase signature
88 112 InterPro IPR001260 Coproporphyrinogen III oxidase, aerobic
29 45 PRINTS PR00073 Coprogen oxidase signature
29 45 InterPro IPR001260 Coproporphyrinogen III oxidase, aerobic
160 189 PRINTS PR00073 Coprogen oxidase signature
160 189 InterPro IPR001260 Coproporphyrinogen III oxidase, aerobic
260 286 PRINTS PR00073 Coprogen oxidase signature
260 286 InterPro IPR001260 Coproporphyrinogen III oxidase, aerobic
232 259 PRINTS PR00073 Coprogen oxidase signature
232 259 InterPro IPR001260 Coproporphyrinogen III oxidase, aerobic
4 298 SUPERFAMILY SSF102886 Coproporphyrinogen III oxidase
4 298 InterPro IPR036406 Oxygen-dependent coproporphyrinogen III oxidase superfamily
2 275 Hamap MF_00333 Oxygen-dependent coproporphyrinogen-III oxidase [hemF].
2 275 InterPro IPR001260 Coproporphyrinogen III oxidase, aerobic
1 299 FunFam G3DSA:3.40.1500.10:FF:000001 Oxygen-dependent coproporphyrinogen-III oxidase
7 298 Pfam PF01218 Coproporphyrinogen III oxidase
7 298 InterPro IPR001260 Coproporphyrinogen III oxidase, aerobic

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 · FPocket

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

Site 1 FPocket #23
0.943
Unusual size
Show in viewer
Surrounding area
Site 2 FPocket #5
0.339
Likely same site as P2Rank 1 2.5 Å 34 shared residues 87% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

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

Site 1 P2Rank #1
0.986
Likely same site as FPocket 5 2.5 Å 34 shared residues 87% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.107
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.078
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.021
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:106-106 Proton donor
UniProt: Binding site:106-106
UniProt: Binding site:108-110
UniProt: Binding site:145-145
UniProt: Binding site:175-175
UniProt: Binding site:258-260
UniProt: Binding site:92-92
UniProt: Binding site:96-96
UniProt: Site:175-175 Important for dimerization
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_A0A0H3GVY6
AlphaFold DB full sequence Viewing
ColabFold KP13_03535
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.

53 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 1 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
0PA PDB via homolog 128.2 Da · LogP 1.65 · TPSA 37.3 Open detail RCSB PDB
FIC PDB via homolog Detail RCSB PDB
CHEMBL2270643 ChEMBL via homolog · pchembl 8.52 (~3.0 nM) Detail ChEMBL
ZINC391863 ZINC proposed compound · Tanimoto 0.778 Detail ZINC
ZINC138516278 ZINC proposed compound · Tanimoto 0.730 Detail ZINC

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
0PA RCSB PDB P84155 128.2 Da LogP 1.65 TPSA 37.3 ✓ Ro5 ✓ Clean C1CCC(C1)CC(=O)O
FIC RCSB PDB P84155 179.1 Da LogP 2.01 TPSA 53.1 ✓ Ro5 ✓ Clean c1cc2c(cc1F)cc([nH]2)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.