KpATCC43816 Protein target profile

peptidase M16 inactive domain protein

Accession: VK055_4295

Gene: AIK82840.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GXU7
Length 950
Pocket druggability (P2Rank · AlphaFold DB model) 0.688
Direct ligand evidence 0 78 total records
Functional annotation 1 EC 4 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 (%)
33.981 Lower values reduce human off-target concern.
Human E-value
5.05e-06
Gut microbiome similarity
2.1% 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
93.95 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) 0.688
Structure A0A0H3GXU7
Pocket Pocket 1
Druggability (FPocket) 0.797
Structure A0A0H3GXU7
Pocket Pocket 2
ColabFold model
P2Rank 0.601 · Pocket 1
FPocket 0.335 · Pocket 6
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 101 / 4744 genomes with a hit
Prevalence 2.1%

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.

MLAALWAPFSQADTGWQPIQETIRKSEKDTRQYQAIRLDNDMVVLLVSDPQAVKSLSALVVPVGSLQDPADHQGLAHFLEHMTLMGSQKYPQPDSLAEFLKLHGGSHNASTAPYRTAFYLEVENDALDGAVDRLADAIAAPLLDKKYADRERNAVNAELTMARTRDGMRMAQVSAETINPAHPAAHFSGGNLETLSDKPGSPVLDALHTFRDSWYSANLMKAVIYSNKPLPALARMAADTFGRVPNRQISRPDITVPVVTDAQKGIIIHYVPAMPRKVLRVEFRIDNNSDRFRSKTDELVTYLIGNRSPGTLSDWLQKQGLAEGIRADSDPVVNGNSGVLAISATLTDKGLAHRDEVTAAIFSYLDLLRTQGIDKRYFDELAHVLALDFRYPSINRDMDYVEWLADTMIRVPVEHALDVVNIADQYDPQAIKDRLAMMTPQNARIWYISPQEPHNKTAYFVDAPYQVDKISEQTFADWQHKSQAIQLQLPALNPYIPDDFTLIKSDKAWPHPQLILDEPTLRVVYAPSQYFASEPKADISLVLRNPQAMDSARRQVMFALNDYLAGIALDQLSNQAAVGGISFSTGANNGLMVNANGYTQHLPALFSDLLQGYFSYTPTEEQLEQAKSWYAQMMDSAEKGKAYDQAIMPIQMVSQVPYFQREVRRALLPSITLKEVLDYRANLKTRGRPELMVIGNMTADAATTLARQIQQQLGADGNEWCRNKDVVVNRQQLAIFNKAGNSTDSALAAVFAPPNVDEFSSTAASTLLGQIIQPWFYNQLRTEEQLGYAVFAFPMNVGRQWGMGFLLQSSDKQPAFLWQRFQAFFPTAEAKLRAMKPEEFAQLQQAVISQMLQAPQTLGDEASKLSKDFDRGNMRFDSRDKVVAQIKLLTPQKLADFFHQTVVDPQGMTILSQISGSQNGKADYAQPKGGKVWENVSALQQSLPLMRENE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization
Periplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain 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.
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0046872 Binding to a metal ion.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

29 records
Show feature table
Start End DB Term Name
204 381 Pfam PF05193 Peptidase M16 inactive domain
204 381 InterPro IPR007863 Peptidase M16, C-terminal
670 845 Pfam PF05193 Peptidase M16 inactive domain
670 845 InterPro IPR007863 Peptidase M16, C-terminal
22 251 SUPERFAMILY SSF63411 LuxS/MPP-like metallohydrolase
22 251 InterPro IPR011249 Metalloenzyme, LuxS/M16 peptidase-like
2 7 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
8 12 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
20 901 PANTHER PTHR43690 NARDILYSIN
64 87 ProSitePatterns PS00143 Insulinase family, zinc-binding region signature.
64 87 InterPro IPR001431 Peptidase M16, zinc-binding site
1 12 Phobius SIGNAL_PEPTIDE Signal peptide region
726 946 SUPERFAMILY SSF63411 LuxS/MPP-like metallohydrolase
726 946 InterPro IPR011249 Metalloenzyme, LuxS/M16 peptidase-like
13 260 Gene3D G3DSA:3.30.830.10 -
13 249 FunFam G3DSA:3.30.830.10:FF:000012 Protease 3
13 950 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
261 491 Gene3D G3DSA:3.30.830.10 -
493 874 Gene3D G3DSA:3.30.830.10 -
389 662 Pfam PF16187 Middle or third domain of peptidase_M16
389 662 InterPro IPR032632 Peptidase M16, middle/third domain
1 1 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
641 906 Gene3D G3DSA:3.30.830.10 -
493 718 SUPERFAMILY SSF63411 LuxS/MPP-like metallohydrolase
493 718 InterPro IPR011249 Metalloenzyme, LuxS/M16 peptidase-like
254 491 SUPERFAMILY SSF63411 LuxS/MPP-like metallohydrolase
254 491 InterPro IPR011249 Metalloenzyme, LuxS/M16 peptidase-like
43 180 Pfam PF00675 Insulinase (Peptidase family M16)
43 180 InterPro IPR011765 Peptidase M16, N-terminal

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
0.688
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Surrounding area
Pocket 2 P2Rank #2
0.342
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Surrounding area
Pocket 3 P2Rank #3
0.237
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Surrounding area
Pocket 4 P2Rank #4
0.216
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Surrounding area
Pocket 5 P2Rank #5
0.197
Likely same site as FPocket 13 3.6 Å 12 shared residues 100% of smaller site
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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 #2
0.797
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Surrounding area
Pocket 2 FPocket #70
0.505
Show in viewer
Surrounding area
Pocket 3 FPocket #13
0.346 Unusual size
Likely same site as P2Rank 5 3.6 Å 12 shared residues 100% of smaller site
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Surrounding area
Pocket 4 FPocket #3
0.278 Unusual size
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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_A0A0H3GXU7
AlphaFold DB full sequence Viewing
ColabFold VK055_4295
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.

78 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 28 records from similar proteins
Structural ligands 16 0 loaded crystals
Measured bioactivity 12 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1EF PDB via homolog 443.5 Da · LogP 3.35 · TPSA 109.1 Open detail RCSB PDB
2H7 PDB via homolog Detail RCSB PDB
2PJ PDB via homolog Detail RCSB PDB
2Q6 PDB via homolog Detail RCSB PDB
2QW 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
1EF RCSB PDB P14735 443.5 Da LogP 3.35 TPSA 109.1 ✓ Ro5 ✓ Clean Cc1ccc(cc1)C(=O)NCc2cn(nn2)[C@H](Cc3ccc4ccccc4c…
2H7 RCSB PDB P14735 447.5 Da LogP 3.18 TPSA 109.1 ✓ Ro5 ✓ Clean c1ccc2cc(ccc2c1)C[C@H](CC(=O)NO)n3cc(nn3)CNC(=O…
2PJ RCSB PDB P14735 398.5 Da LogP 5.36 TPSA 51.2 1 viol. ✓ Clean CC(C)(C)OC(=O)NC[C@@H](Cc1cc2ccccc2nc1)c3cc(ccc…
2Q6 RCSB PDB P14735 734.0 Da LogP 7.55 TPSA 135.9 2 viol. ✓ Clean COC(=O)NC[C@@H](Cc1cc2ccccc2nc1)c3ccc(cc3)OCCCC…
2QW RCSB PDB P14735 424.4 Da LogP 2.89 TPSA 84.2 ✓ Ro5 ✓ Clean Cc1ccc(cc1)NC(=O)[C@H](C2CCCCC2)NC(=O)[C@H](CC[…
2QX RCSB PDB P14735 735.9 Da LogP 7.85 TPSA 126.6 2 viol. ✓ Clean COC(=O)NC[C@@H](Cc1cc2ccccc2nc1)c3cc(ccc3F)CCCC…
33K RCSB PDB P14735 360.4 Da LogP 0.11 TPSA 135.6 ✓ Ro5 ✓ Clean c1ccc(cc1)CN(CC(=O)N[C@@H](Cc2cnc[nH]2)C(=O)O)C…
3M9 RCSB PDB P14735 447.5 Da LogP 3.18 TPSA 109.1 ✓ Ro5 ✓ Clean c1ccc2cc(ccc2c1)C[C@H](CC(=O)NO)n3c(cnn3)CNC(=O…
I41 RCSB PDB P14735 374.4 Da LogP 0.20 TPSA 124.6 ✓ Ro5 ✓ Clean COC(=O)[C@H](Cc1cnc[nH]1)NC(=O)C[N@](Cc2ccccc2)…
J18 RCSB PDB P14735 558.7 Da LogP 5.60 TPSA 60.9 2 viol. ✓ Clean Cc1cccc(c1C)c2ccc(cc2)[C@H]3[C@@H]4CN(CCCCN4[C@…
J22 RCSB PDB P14735 494.7 Da LogP 3.32 TPSA 78.7 ✓ Ro5 ✓ Clean Cc1cccc(c1C)c2ccc(cc2)[C@H]3[C@@H]4CN(CCCCN4[C@…
MGH RCSB PDB P14735 416.4 Da LogP 0.16 TPSA 141.7 ✓ Ro5 ✓ Clean COC(=O)[C@@H](Cc1c[nH]cn1)NC(=O)CN(CC(=O)O)C(=O…
MGJ RCSB PDB P14735 401.5 Da LogP 0.20 TPSA 127.4 ✓ Ro5 ✓ Clean CNC(=O)[C@H](Cc1c[nH]cn1)NC(=O)C[N@](CCCc2ccccc…
MGK RCSB PDB P14735 402.5 Da LogP 0.63 TPSA 124.6 ✓ Ro5 ✓ Clean COC(=O)[C@H](Cc1cnc[nH]1)NC(=O)C[N@](CCCc2ccccc…
MGW RCSB PDB P14735 388.4 Da LogP 0.24 TPSA 124.6 ✓ Ro5 ✓ Clean COC(=O)[C@H](Cc1cnc[nH]1)NC(=O)C[N@@](CCc2ccccc…
QIX RCSB PDB P14735 542.6 Da LogP -1.64 TPSA 241.6 2 viol. ✓ Clean [H]/N=C(/N)\NCCC[C@@H](C(=O)NCC(=O)NCC(=O)N)NC(…

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.