KpATCC43816 Protein target profile

dipeptidase AC. Metallo peptidase

Accession: VK055_0680

Gene: AIK79303.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GTU1
Length 339
Pocket druggability (P2Rank · AlphaFold DB model) 0.797
Direct ligand evidence 0 157 total records
Functional annotation 0 EC 2 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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 (%)
28.261 Lower values reduce human off-target concern.
Human E-value
9.92e-08
Gut microbiome similarity
0.5% 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
96.52 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) 0.797
Structure A0A0H3GTU1
Pocket Pocket 1
Druggability (FPocket) 0.315
Structure A0A0H3GTU1
Pocket Pocket 14
ColabFold model
P2Rank 0.798 · Pocket 1
FPocket 0.292 · Pocket 8
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 25 / 4744 genomes with a hit
Prevalence 0.5%

Metabolic context

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

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MAIFDGHNDLLLNLWLHHREDPVSAFFAGIENGHLDYPRMLQGGFAGGLFALFVPPQEYIARMTPQYASQRWDPIDILWQQLAILKQLIAHSAGRLRLCLSAADIERCREDKVLAMVAHIEGAGGFDGEGRDLHAFYAAGVRSIGPFWNIANRFGSGVNGSFPGSPDTGPGLTAAGIDLIKQVNALKMQMDVSHMNEKAFWDTAHHSTSPLVATHSNAHALCPQPRNLTDQQLRAIRDSGGVVGVNFGNAFLRADGRRDSDTPLTTIVRHIDYLINIMGEDHVALGSDFDGITLPDELGDVAGLPRLINTLRASGYDQLVLDKLLWRNWLRVLKNFWQQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

2 GO

Subcellular localization

Localization
Unknown

Gene Ontology (GO)

2
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • 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.

11 records
Show feature table
Start End DB Term Name
2 334 Pfam PF01244 Membrane dipeptidase (Peptidase family M19)
2 334 InterPro IPR008257 Peptidase M19
1 337 SUPERFAMILY SSF51556 Metallo-dependent hydrolases
1 337 InterPro IPR032466 Metal-dependent hydrolase
3 332 CDD cd01301 rDP_like
3 332 InterPro IPR008257 Peptidase M19
1 339 Gene3D G3DSA:3.20.20.140 -
1 339 ProSiteProfiles PS51365 Renal dipeptidase family profile.
1 339 InterPro IPR008257 Peptidase M19
3 337 PANTHER PTHR10443 MICROSOMAL DIPEPTIDASE
3 337 InterPro IPR008257 Peptidase M19

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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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 · P2Rank

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

Pocket 1 P2Rank #1
0.797
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.426
Likely same site as FPocket 14 0.7 Å 10 shared residues 91% of smaller site
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.066
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #14
0.315
Likely same site as P2Rank 2 0.7 Å 10 shared residues 91% of smaller site
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_A0A0H3GTU1
AlphaFold DB full sequence Viewing
ColabFold VK055_0680
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.

157 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 107 records from similar proteins
Structural ligands 7 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
B88 PDB via homolog 239.2 Da · LogP -0.26 · TPSA 137.9 Open detail RCSB PDB
L3A PDB via homolog Detail RCSB PDB
LDE PDB via homolog Detail RCSB PDB
LY0 PDB via homolog Detail RCSB PDB
P4D 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
B88 RCSB PDB Q93J45 239.2 Da LogP -0.26 TPSA 137.9 ✓ Ro5 ✓ Clean C[C@H](N)[P@](=O)(C[C@@H](CC(=O)O)C(=O)O)O
L3A RCSB PDB Q93J45 237.2 Da LogP 1.31 TPSA 100.6 ✓ Ro5 ✓ Clean C[C@@H](CP(=O)([C@H](CC(C)C)N)O)C(=O)O
LDE RCSB PDB Q93J45 295.3 Da LogP 1.15 TPSA 137.9 ✓ Ro5 ✓ Clean CC(C)C[C@H](N)P(=O)(C[C@H](CCC(=O)O)C(=O)O)O
LY0 RCSB PDB Q3IZQ3 195.2 Da LogP 0.28 TPSA 100.6 ✓ Ro5 ✓ Clean C[C@@H](C[P@](=O)([C@H](C)N)O)C(=O)O
P4D RCSB PDB Q93J45 331.3 Da LogP 0.67 TPSA 158.2 ✓ Ro5 ✓ Clean c1cc(ccc1C[C@H](N)P(=O)(C[C@H](CC(=O)O)C(=O)O)O…
P5D RCSB PDB Q93J45 315.3 Da LogP 0.96 TPSA 137.9 ✓ Ro5 ✓ Clean c1ccc(cc1)C[C@H](N)P(=O)(C[C@H](CC(=O)O)C(=O)O)O
P8D RCSB PDB Q93J45 239.2 Da LogP -0.26 TPSA 137.9 ✓ Ro5 ✓ Clean C[C@H](N)[P@@](=O)(C[C@H](CC(=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.

Cross-references

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

Chemistry

ChEMBL CHEMBL119723 ChEMBL CHEMBL117337 ChEMBL CHEMBL326292 ChEMBL CHEMBL333841 ChEMBL CHEMBL11661 ChEMBL CHEMBL119055 ChEMBL CHEMBL274188 ChEMBL CHEMBL332970 ChEMBL CHEMBL334279 ChEMBL CHEMBL120600 ChEMBL CHEMBL268228 ChEMBL CHEMBL334143 ChEMBL CHEMBL11747 ChEMBL CHEMBL332290 ChEMBL CHEMBL12008 ChEMBL CHEMBL122415 ChEMBL CHEMBL274846 ChEMBL CHEMBL12095 ChEMBL CHEMBL12001 ChEMBL CHEMBL1907817 ChEMBL CHEMBL119261 ChEMBL CHEMBL12086 ChEMBL CHEMBL1907823 ChEMBL CHEMBL11951 ChEMBL CHEMBL276215 ChEMBL CHEMBL11554 ChEMBL CHEMBL11961 ChEMBL CHEMBL275227 ChEMBL CHEMBL12037 ChEMBL CHEMBL325021 ChEMBL CHEMBL11482 ChEMBL CHEMBL11992 ChEMBL CHEMBL12141 ChEMBL CHEMBL273413 ChEMBL CHEMBL273511 ChEMBL CHEMBL766 ChEMBL CHEMBL11556 ChEMBL CHEMBL11602 ChEMBL CHEMBL11777 ChEMBL CHEMBL11543 ChEMBL CHEMBL11830 ChEMBL CHEMBL11930 ChEMBL CHEMBL11967 ChEMBL CHEMBL120198 ChEMBL CHEMBL1237318 ChEMBL CHEMBL1907816 ChEMBL CHEMBL273926 ChEMBL CHEMBL275319 ChEMBL CHEMBL11941 ChEMBL CHEMBL1907822 ChEMBL CHEMBL275571 ChEMBL CHEMBL417431 ChEMBL CHEMBL417981 ChEMBL CHEMBL273925 ChEMBL CHEMBL428006 ChEMBL CHEMBL11674 ChEMBL CHEMBL12126 ChEMBL CHEMBL12195 ChEMBL CHEMBL1907818 ChEMBL CHEMBL429369 ChEMBL CHEMBL119118 ChEMBL CHEMBL276162 ChEMBL CHEMBL420537 ChEMBL CHEMBL11763 ChEMBL CHEMBL11704 ChEMBL CHEMBL274903 ChEMBL CHEMBL11324 ChEMBL CHEMBL11792 ChEMBL CHEMBL11925 ChEMBL CHEMBL274139 ChEMBL CHEMBL275318 ChEMBL CHEMBL12353 ChEMBL CHEMBL118190 ChEMBL CHEMBL11918 ChEMBL CHEMBL11996 ChEMBL CHEMBL11242 ChEMBL CHEMBL11887 ChEMBL CHEMBL11997 ChEMBL CHEMBL11971 ChEMBL CHEMBL273954 ChEMBL CHEMBL11569 ChEMBL CHEMBL11764 ChEMBL CHEMBL267101 ChEMBL CHEMBL119392 ChEMBL CHEMBL11321 ChEMBL CHEMBL11924 ChEMBL CHEMBL268273 ChEMBL CHEMBL417797 ChEMBL CHEMBL11876 ChEMBL CHEMBL11481 ChEMBL CHEMBL3559630 ChEMBL CHEMBL11649 ChEMBL CHEMBL12075 ChEMBL CHEMBL11969 ChEMBL CHEMBL12080 ChEMBL CHEMBL11744 ChEMBL CHEMBL3559635 ChEMBL CHEMBL267768 ChEMBL CHEMBL3559476 ChEMBL CHEMBL12009