KpKP13 Protein target profile

Imidazolonepropionase

Accession: KP13_03018

Gene: AHE45598.1 hutI 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GQF7
Length 439
Pocket druggability (P2Rank · AlphaFold DB model) 0.878
Direct ligand evidence 0 57 total records
Functional annotation 1 EC 9 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 (%)
34.085 Lower values reduce human off-target concern.
Human E-value
1.4399999999999994e-54
Gut microbiome similarity
2.6% 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.

Structure confidence

ColabFold pLDDT
91.37 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) 0.878
Structure A0A0H3GQF7
Pocket Pocket 1
Druggability (FPocket) 0.465
Structure A0A0H3GQF7
Pocket Pocket 14
ColabFold model
P2Rank 0.884 · Pocket 1
FPocket 0.471 · Pocket 13
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 125 / 4744 genomes with a hit
Prevalence 2.6%

Sequence

Primary amino-acid sequence viewer.

MVFSHKKITFPCAIVDFTGVMKINVYTTHDKLSAMTEATSELVIWRNGRLATLNPDHAQPYGLLERHALLVRDGRIAAIVAEDDVPSGRSIDLEGRLVTPGLIDCHTHLVFGGSRAQEWEQRLNGVSYQTISASGGGINSTVRATRDSSEAELLALAQPRLERLLREGVTTLEIKSGYGLDLPNERKMLRVARQLADHNGVELSATLLSAHATPPEYQGDADGYITLVCETILPTLWQEGLFESVDVFCENVGFSPQQTERVFQAAQALGIPVKGHVEQLSSLGGAQLVSRYHGLSADHIEYLTEEGVAAMRESGTVAALLPGAFYFLNETRKPPVELLRKYQVPMAVATDFNPGTSPFASLHLAMNMACVKFGLTPEEAWAGVTRHAARALGRQASHGQLAPGFVANFAIWDAEHPVEMVYEPGRSPLWHRVVQGELQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016810 Catalysis of the hydrolysis of any carbon-nitrogen bond, C-N, with the exception of peptide bonds.
  • GO:0019556 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including glutamate and formamide.
  • GO:0016812 Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a cyclic amide.
  • GO:0050480 Catalysis of the reaction: (S)-3-(4-oxo-4,5-dihydro-1H-imidazol-5-yl)propanoic acid + H2O = N-formimidoyl-L-glutamate + H+.
  • GO:0005506 Binding to an iron (Fe) ion.
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0019557 OBSOLETE. The chemical reactions and pathways resulting in the breakdown of L-histidine into other compounds, including glutamate and formate.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

18 records
Show feature table
Start End DB Term Name
65 437 NCBIfam TIGR01224 imidazolonepropionase
65 437 InterPro IPR005920 Imidazolonepropionase
43 438 SUPERFAMILY SSF51338 Composite domain of metallo-dependent hydrolases
43 438 InterPro IPR011059 Metal-dependent hydrolase, composite domain superfamily
97 417 Pfam PF01979 Amidohydrolase family
97 417 InterPro IPR006680 Amidohydrolase-related
101 399 FunFam G3DSA:3.20.20.140:FF:000007 Imidazolonepropionase
100 399 SUPERFAMILY SSF51556 Metallo-dependent hydrolases
100 399 InterPro IPR032466 Metal-dependent hydrolase
48 436 Gene3D G3DSA:2.30.40.10 Urease, subunit C, domain 1
48 436 InterPro IPR011059 Metal-dependent hydrolase, composite domain superfamily
69 425 CDD cd01296 Imidazolone-5PH
69 425 InterPro IPR005920 Imidazolonepropionase
101 399 Gene3D G3DSA:3.20.20.140 -
41 439 Hamap MF_00372 Imidazolonepropionase [hutI].
41 439 InterPro IPR005920 Imidazolonepropionase
35 437 PANTHER PTHR42752 IMIDAZOLONEPROPIONASE
35 437 InterPro IPR005920 Imidazolonepropionase

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 · P2Rank

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

Pocket 1 P2Rank #1
0.878
Likely same site as FPocket 14 1.3 Å 20 shared residues 100% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.107
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Surrounding area
Pocket 3 P2Rank #3
0.028
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Surrounding area
Pocket 4 P2Rank #4
0.005
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Surrounding area
Pocket 5 P2Rank #5
0.005
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #14
0.465
Likely same site as P2Rank 1 1.3 Å 20 shared residues 100% of smaller site
Show in viewer
Surrounding area
Residue sets
UniProt: Binding site:106-106
UniProt: Binding site:108-108
UniProt: Binding site:115-115
UniProt: Binding site:178-178
UniProt: Binding site:211-211
UniProt: Binding site:276-276
UniProt: Binding site:279-279
UniProt: Binding site:351-351
UniProt: Binding site:353-353
UniProt: Binding site:355-355
UniProt: Binding site:356-356
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_A0A0H3GQF7
AlphaFold DB full sequence Viewing
ColabFold KP13_03018
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.

57 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 7 records from similar proteins
Structural ligands 4 0 loaded crystals
Measured bioactivity 3 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
DI6 PDB via homolog 172.1 Da · LogP -0.94 · TPSA 95.5 Open detail RCSB PDB
IZC PDB via homolog Detail RCSB PDB
NCD PDB via homolog Detail RCSB PDB
NIG PDB via homolog Detail RCSB PDB
CHEMBL4532317 ChEMBL via homolog Detail ChEMBL

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
DI6 RCSB PDB A0KF84 172.1 Da LogP -0.94 TPSA 95.5 ✓ Ro5 ✓ Clean C(CC(=O)O)[C@H]1C(=O)NC(=O)N1
IZC RCSB PDB P42084 126.1 Da LogP -0.06 TPSA 62.0 ✓ Ro5 ✓ Clean C1N=CC(=N1)CC(=O)O
NCD RCSB PDB Q81WF0 176.1 Da LogP -1.42 TPSA 129.7 ✓ Ro5 ✓ Clean C([C@@H](C(=O)O)NC(=O)N)C(=O)O
NIG RCSB PDB Q8U8Z6 174.2 Da LogP -0.50 TPSA 110.5 ✓ Ro5 ✓ Clean [H]/N=C\N[C@@H](CCC(=O)O)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.

Cross-references

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