KpKP13 Protein target profile

Aminoacyl-histidine dipeptidase

Accession: KP13_31631

Gene: pepD AHE46191.1 3D evidence: AlphaFold DB model + ColabFold model UniProt A0A0H3GJV8
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Length 485
Pocket druggability (P2Rank · AlphaFold DB model) 0.923
Direct ligand evidence 0 17 total records
Functional annotation 1 EC 5 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. Moderate predicted binding pocket FPocket selected-pocket score 0.47. This supports review but is not experimental validation. Second pocket predictor agrees P2Rank predicted binding-site probability 0.92. Review the complete evidence below

Risks to review

Microbiome similarity 160 of 4744 screened genomes (3.4%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.92) — check the ligand evidence before deprioritizing on off-target risk alone. Only proposed compounds 17 ZINC similarity-based candidates, no stronger ligand evidence.

Evidence gaps

No metabolic context No SBML/network-derived reaction evidence is loaded for 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
No hit
Gut microbiome similarity
3.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
96.26 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) 0.923
Structure A0A0H3GJV8
Pocket Pocket 1
Druggability (FPocket) 0.474
Structure A0A0H3GJV8
Pocket Pocket 16
ColabFold model
P2Rank 0.941 · Pocket 1
FPocket 0.594 · Pocket 14
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 160 / 4744 genomes with a hit
Prevalence 3.4%

Sequence

Primary amino-acid sequence viewer.

MSELSQLSPQPLWDIFAKICSIPHPSYHEEQLAEHIMGWAKEKGLHAERDQVGNILIRKGATAGMENRKPVALQAHLDMVPQKNNDTVHDFVKDPIQPYIDGEWVKARGTTLGADNGIGMASALAVLADDSVAHGPLEVLLTMTEEAGMDGAFGLQANWLQADILINTDSEEEGEIYMGCAGGIDFTSNLALTREAIPAGFQSFKVTLKGLKGGHSGGDIHLGLGNANKLLSRFLAGHADELDLRLVDFNGGTLRNAIPREAYATVAVAADKADALKALVNTYQALLKNELEANEKNLVVLLEAVDNDKAALTQASRDTFIRLLNATPNGVIRNSDVAKGVVETSLNVGVVTMTDDNVQIHCLIRSLIDSGKDYVVSMLDSLGKLAGAKTEAKGAYPGWQPDANSPVMHLVRETYQRLFNKTPNIQIIHAGLECGLFKKPYPEMDMVSIGPTITGPHSPDEQVHIESVGQYWTLLTELLKAIPAK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0016787 Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc.
  • 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:0070573 Catalysis of the hydrolysis of a dipeptide by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
1 484 PANTHER PTHR43501 CYTOSOL NON-SPECIFIC DIPEPTIDASE
1 484 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
368 485 Gene3D G3DSA:3.40.630.10 Zn peptidases
1 233 Gene3D G3DSA:3.40.630.10 Zn peptidases
1 485 PIRSF PIRSF016599 Xaa-His_dipept
1 485 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
8 482 NCBIfam TIGR01893 beta-Ala-His dipeptidase
8 482 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
9 482 CDD cd03890 M20_pepD
9 482 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
203 293 Pfam PF07687 Peptidase dimerisation domain
203 293 InterPro IPR011650 Peptidase M20, dimerisation domain
428 444 PRINTS PR00934 X-His dipeptidase (M25) signature
428 444 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
80 99 PRINTS PR00934 X-His dipeptidase (M25) signature
80 99 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
450 472 PRINTS PR00934 X-His dipeptidase (M25) signature
450 472 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
363 381 PRINTS PR00934 X-His dipeptidase (M25) signature
363 381 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
206 223 PRINTS PR00934 X-His dipeptidase (M25) signature
206 223 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
101 119 PRINTS PR00934 X-His dipeptidase (M25) signature
101 119 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
135 152 PRINTS PR00934 X-His dipeptidase (M25) signature
135 152 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
159 177 PRINTS PR00934 X-His dipeptidase (M25) signature
159 177 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
251 270 PRINTS PR00934 X-His dipeptidase (M25) signature
251 270 InterPro IPR001160 Peptidase M20C, Xaa-His dipeptidase
368 484 FunFam G3DSA:3.40.630.10:FF:000018 Aminoacyl-histidine dipeptidase PepD
72 480 Pfam PF01546 Peptidase family M20/M25/M40
72 480 InterPro IPR002933 Peptidase M20
1 238 FunFam G3DSA:3.40.630.10:FF:000015 Aminoacyl-histidine dipeptidase PepD
10 481 SUPERFAMILY SSF53187 Zn-dependent exopeptidases

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
0.923
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Surrounding area
Pocket 2 P2Rank #2
0.173
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.132
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.007
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #16
0.474
Show in viewer
Surrounding area
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_A0A0H3GJV8
AlphaFold DB — — full sequence — Viewing
ColabFold KP13_31631
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.

17 records
Chemistry signal

Only proposed virtual-screening candidates are available for this target.

Direct evidence 0 same-protein records
Transferred evidence 0 records from similar proteins
Structural ligands 0 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 17 similarity-based ZINC candidates
Best available ligand signal
ZINC1532902 ZINC proposed compound Tanimoto 0.700 206.2 Da · LogP -0.86 · TPSA 132.1 Open detail ZINC
ZINC2018106 ZINC proposed compound · Tanimoto 0.700 Detail ZINC
ZINC3593496 ZINC proposed compound · Tanimoto 0.652 Detail ZINC
ZINC3593497 ZINC proposed compound · Tanimoto 0.652 Detail ZINC
ZINC14686440 ZINC proposed compound · Tanimoto 0.625 Detail ZINC

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Show only:
Ligand Tanimoto MW · LogP · TPSA Lipinski PAINS SMILES
ZINC1532902 ZINC 0.700 206.2 Da LogP -0.86 TPSA 132.1 ✓ Ro5 ✓ Clean O=C(O)CC[C@@](O)(CC(=O)O)C(=O)O
ZINC2018106 ZINC 0.700 206.2 Da LogP -0.86 TPSA 132.1 ✓ Ro5 ✓ Clean O=C(O)CC[C@](O)(CC(=O)O)C(=O)O
ZINC3593496 ZINC 0.652 206.2 Da LogP -1.16 TPSA 121.1 ✓ Ro5 ✓ Clean COC(=O)C[C@@](O)(CC(=O)O)C(=O)O
ZINC3593497 ZINC 0.652 206.2 Da LogP -1.16 TPSA 121.1 ✓ Ro5 ✓ Clean COC(=O)C[C@](O)(CC(=O)O)C(=O)O
ZINC14686440 ZINC 0.625 436.4 Da LogP -2.64 TPSA 247.9 1 viol. ✓ Clean O=C(O)C[C@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=O…
ZINC14686442 ZINC 0.625 436.4 Da LogP -2.64 TPSA 247.9 1 viol. ✓ Clean O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@](O)(CC(=O…
ZINC14686444 ZINC 0.625 436.4 Da LogP -2.64 TPSA 247.9 1 viol. ✓ Clean O=C(O)C[C@@](O)(CC(=O)NCCCCNC(=O)C[C@@](O)(CC(=…
ZINC13398039 ZINC 0.577 234.2 Da LogP -0.38 TPSA 121.1 ✓ Ro5 ✓ Clean CC(C)OC(=O)C[C@](O)(CC(=O)O)C(=O)O
ZINC2528012 ZINC 0.577 234.2 Da LogP -0.38 TPSA 121.1 ✓ Ro5 ✓ Clean CC(C)OC(=O)C[C@@](O)(CC(=O)O)C(=O)O
ZINC146315135 ZINC 0.560 204.2 Da LogP 0.86 TPSA 94.8 ✓ Ro5 ✓ Clean CCCCC[C@@](O)(CC(=O)O)C(=O)O
ZINC146315336 ZINC 0.560 204.2 Da LogP 0.86 TPSA 94.8 ✓ Ro5 ✓ Clean CCCCC[C@](O)(CC(=O)O)C(=O)O
ZINC1850353 ZINC 0.556 206.1 Da LogP -0.86 TPSA 132.1 ✓ Ro5 ✓ Clean O=C(O)CC(O)(CC(=O)O)CC(=O)O
ZINC13398014 ZINC 0.522 220.2 Da LogP -1.07 TPSA 110.1 ✓ Ro5 ✓ Clean COC(=O)CC(O)(CC(=O)OC)C(=O)O
ZINC3861629 ZINC 0.522 206.1 Da LogP -1.16 TPSA 121.1 ✓ Ro5 ✓ Clean COC(=O)C(O)(CC(=O)O)CC(=O)O
ZINC100969993 ZINC 0.500 359.5 Da LogP 2.70 TPSA 123.9 ✓ Ro5 ✓ Clean CCCCCCCCCCCCNC(=O)C[C@](O)(CC(=O)O)C(=O)O
ZINC100969996 ZINC 0.500 359.5 Da LogP 2.70 TPSA 123.9 ✓ Ro5 ✓ Clean CCCCCCCCCCCCNC(=O)C[C@@](O)(CC(=O)O)C(=O)O
ZINC1711854 ZINC 0.500 248.2 Da LogP -0.13 TPSA 149.2 ✓ Ro5 ✓ Clean O=C(O)CC(CC(=O)O)(CC(=O)O)CC(=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 A0A0H3GJV8