Protein target profile

KP13_05384

Catalase HPII

Genome: KpKP13 Gene: katE AHE45029.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GVY8
Length 752
Pocket druggability 0.972
Direct ligand evidence 0 58 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 (%)
41.016 Lower values reduce human off-target concern.
Human E-value
1.41e-114
Gut microbiome similarity
3.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
80.851 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
97.05 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 0.972
Structure A0A0H3GVY8
Pocket Pocket 1
P2Rank 0.934
Structure A0A0H3GVY8
Pocket Pocket 1
ColabFold model
FPocket 0.953 · Pocket 1
P2Rank 0.969 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 140 / 4744 genomes with a hit
Prevalence 3.0%

Cross-references

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

Sequence

Primary amino-acid sequence viewer.

MSDKHPNPHQQQAPVHDSEEAQPGLDSLAPDDREWRPTPKPTAPGVEPTAPGSLKAPDTHNSKLDSLEAQRKGGEDFPLTTNQGVRIADDQNSLRAGSRGPTLLEDFILREKITHFDHERIPERIVHARGSAAHGYFQPYKSLAALTKADFLSSADKITPVFVRFSTVQGGAGSADTVRDIRGFATKFYTDEGIFDLVGNNTPVFFIQDAMKFPDFVHAVKPEPHWAIPQGQSAHDTFWDYVSLQPETLHNVMWAMSDRGIPRSYRTMEGFGIHTFRLINAEGKATFVRFHWKPVAGKASLVWDEAQKLTGRDPDFHRRDLWEAIEAGDYPEFELGLQLIPEENEFAFDFDLLDPTKLIPEALVPVQRVGRMVLNRNPDNFFAENEQAAFHPGHIVPGIDFSNDPLLQGRLFSYTDTQISRLGGPNFHEIPINRPTCPYHNFQRDGMHRMDIDTNPANYEPNSINDNWPRETPPAAKRGGFESLAERVDGEKIRQRSPSFGEYYAQPRLFWLSQTPIEQQHIIDGFSFELSKVVRTWIRERVVDHLAHIDTKLAEAVGANLGIELSDDQRNITLPAPVNGVEKDPSLSLYADAEGDVKGRVVAVLLNERTSAQDLVQLLQALQAQGVHSKLLYSRMGEVIADDGSPLPIAGTFAGSPSLTVDAVVVPGGDLSALSQSGDARYYLLEAYKHLKPILLAGDARQLTSVLHVPTQGEEGVIVTDALDTPAADKLLALMTAHRVWSRSPKIAAIPA

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:0004096 Catalysis of the reaction: 2 H2O2 = O2 + 2 H2O.
  • GO:0020037 Binding to a heme, a compound composed of iron complexed in a porphyrin (tetrapyrrole) ring.
  • GO:0006979 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
  • 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.
  • GO:0042744 The chemical reactions and pathways resulting in the breakdown of hydrogen peroxide (H2O2).

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

46 records
Show feature table
Start End DB Term Name
599 739 CDD cd03132 GATase1_catalase
599 739 InterPro IPR041399 Large catalase, C-terminal domain
410 418 ProSitePatterns PS00437 Catalase proximal heme-ligand signature.
410 418 InterPro IPR002226 Catalase haem-binding site
41 492 FunFam G3DSA:2.40.180.10:FF:000003 Catalase
1 82 MobiDBLite mobidb-lite consensus disorder prediction
156 174 PRINTS PR00067 Catalase signature
156 174 InterPro IPR018028 Catalase, mono-functional, haem-containing
397 423 PRINTS PR00067 Catalase signature
397 423 InterPro IPR018028 Catalase, mono-functional, haem-containing
177 194 PRINTS PR00067 Catalase signature
177 194 InterPro IPR018028 Catalase, mono-functional, haem-containing
196 214 PRINTS PR00067 Catalase signature
196 214 InterPro IPR018028 Catalase, mono-functional, haem-containing
93 116 PRINTS PR00067 Catalase signature
93 116 InterPro IPR018028 Catalase, mono-functional, haem-containing
365 392 PRINTS PR00067 Catalase signature
365 392 InterPro IPR018028 Catalase, mono-functional, haem-containing
599 752 Gene3D G3DSA:3.40.50.880 -
599 752 InterPro IPR029062 Class I glutamine amidotransferase-like
495 598 Gene3D G3DSA:1.20.1370.20 -
495 598 InterPro IPR043156 Catalase, mono-functional, haem-containing, clade 2, helical domain
80 465 Pfam PF00199 Catalase
80 465 InterPro IPR011614 Catalase core domain
117 561 CDD cd08155 catalase_clade_2
1 17 MobiDBLite mobidb-lite consensus disorder prediction
2 492 Gene3D G3DSA:2.40.180.10 Catalase core domain
43 750 PIRSF PIRSF038927 Catalase_clade2
43 750 InterPro IPR024712 Catalase, mono-functional, haem-containing, clade 2
598 703 SUPERFAMILY SSF52317 Class I glutamine amidotransferase-like
598 703 InterPro IPR029062 Class I glutamine amidotransferase-like
116 132 ProSitePatterns PS00438 Catalase proximal active site signature.
116 132 InterPro IPR024708 Catalase active site
598 745 Pfam PF18011 C-terminal domain found in long catalases
598 745 InterPro IPR041399 Large catalase, C-terminal domain
76 567 ProSiteProfiles PS51402 catalase family profile.
76 567 InterPro IPR018028 Catalase, mono-functional, haem-containing
493 596 FunFam G3DSA:1.20.1370.20:FF:000001 Catalase HPII
498 561 Pfam PF06628 Catalase-related immune-responsive
498 561 InterPro IPR010582 Catalase immune-responsive domain
46 582 SUPERFAMILY SSF56634 Heme-dependent catalase-like
46 582 InterPro IPR020835 Catalase superfamily
80 468 SMART SM01060 Catalase_2
80 468 InterPro IPR011614 Catalase core domain
45 747 PANTHER PTHR42821 CATALASE
45 747 InterPro IPR024712 Catalase, mono-functional, haem-containing, clade 2

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
0.972
Likely same site as P2Rank 1 0.6 Å 22 shared residues 85% 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
0.934
Likely same site as FPocket 1 0.6 Å 22 shared residues 85% of smaller site
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.445
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.408
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.134
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.103
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:127-127
UniProt: Active site:200-200
UniProt: Binding site:124-124
UniProt: Binding site:164-164
UniProt: Binding site:213-213
UniProt: Binding site:410-410
UniProt: Binding site:414-414 axial binding residue
UniProt: Binding site:421-421
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_A0A0H3GVY8
AlphaFold DB full sequence Viewing
ColabFold KP13_05384
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.

58 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 8 records from similar proteins
Structural ligands 8 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
3TR PDB via homolog 84.1 Da · LogP -0.61 · TPSA 67.6 Open detail RCSB PDB
AE3 PDB via homolog Detail RCSB PDB
H2S PDB via homolog Detail RCSB PDB
HDD PDB via homolog Detail RCSB PDB
HDE 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
3TR RCSB PDB M4GGR5 84.1 Da LogP -0.61 TPSA 67.6 ✓ Ro5 ✓ Clean c1[nH]nc(n1)N
AE3 RCSB PDB Q9C169 134.2 Da LogP 0.03 TPSA 38.7 ✓ Ro5 ✓ Clean CCOCCOCCO
H2S RCSB PDB P21179 34.1 Da LogP 0.11 TPSA 0.0 ✓ Ro5 ✓ Clean S
HDD RCSB PDB M4GGR5 632.5 Da LogP 3.21 TPSA 101.9 1 viol. ✓ Clean Cc1c2n3c(c1CCC(=O)O)C=C4[C@]5(CCC(=O)O5)[C@@](C…
HDE RCSB PDB P21179 638.5 Da LogP 4.58 TPSA 101.9 1 viol. ✓ Clean CCc1c(c2n3c1Cc4c(c(c5n4[Fe]36n7c(c(c(c7C=C8N6C(…
O RCSB PDB Q9C169 18.0 Da LogP -0.82 TPSA 31.5 ✓ Ro5 ✓ Clean O
PEO RCSB PDB P21179 34.0 Da LogP 0.02 TPSA 40.5 ✓ Ro5 ✓ Clean OO
TAR RCSB PDB Q9C169 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@H]([C@@H](C(=O)O)O)(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.