KpATCC43816 Protein target profile

aminopeptidase B

Accession: VK055_4646

Gene: AIK83180.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3H1H0
Length 428
Pocket druggability (P2Rank · AlphaFold DB model) 0.738
Direct ligand evidence 0 160 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 (%)
40.164 Lower values reduce human off-target concern.
Human E-value
2.74e-18
Gut microbiome similarity
3.1% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
41.325 Higher values support similarity to known essential genes.
DEG E-value
1.0300000000000001e-57 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
97.83 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) 0.738
Structure A0A0H3H1H0
Pocket Pocket 1
Druggability (FPocket) 0.566
Structure A0A0H3H1H0
Pocket Pocket 23
ColabFold model
P2Rank 0.818 · Pocket 1
FPocket 0.484 · Pocket 28
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 146 / 4744 genomes with a hit
Prevalence 3.1%

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.

MTEAMKITLSTQPADGRWGEKATWSINNDGIALHLNGKDDLGLIQRAARKIDGMGIKHVALSGEGWNTDRAWAFWAGYKGPKGQRQVEWPSLDDAQRSELDNRLTIIDWVRDTINAPAEELGPEQLAQRAVDLLCGVAGEKISYRITKGEDLREQGYLGLHTVGRGSERPPVLLALDYNPTGDKEAPVYACLVGKGITFDSGGYSIKQSAFMDSMKSDMGGAATITGALAFAITRGLNKRVKLFLCCADNLISGNAFKLGDIIHYRNGKTVEVMNTDAEGRLVLADGLIDASAQKPELIIDAATLTGAAKTALGNDYHALFSFDDALANRLLASAQAENEAFWRLPLAEFHRNQLPSNFADLNNTGSAAYPAGASTAAGFLSHFVENYHQGWLHIDCSATYRKSAVEQWSAGATGLGVRTIANLLTAE

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
  • GO:0019538 The chemical reactions and pathways involving a protein. Includes protein modification.
  • GO:0070006 Catalysis of the hydrolysis of a single N-terminal amino acid residue from 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:0046872 Binding to a metal ion.
  • GO:0030145 Binding to a manganese ion (Mn).
  • 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.

27 records
Show feature table
Start End DB Term Name
5 81 Pfam PF12404 Peptidase
5 81 InterPro IPR047620 Peptidase M17, peptidase B-like, N-terminal domain
275 282 ProSitePatterns PS00631 Cytosol aminopeptidase signature.
275 282 InterPro IPR000819 Peptidase M17, leucyl aminopeptidase, C-terminal
84 426 PANTHER PTHR11963 LEUCINE AMINOPEPTIDASE-RELATED
84 426 InterPro IPR011356 Peptidase M17, leucine aminopeptidase/peptidase B
3 427 Hamap MF_00504 Peptidase B [pepB].
3 427 InterPro IPR008330 Peptidase M17, peptidase B
98 428 Gene3D G3DSA:3.40.630.10 Zn peptidases
109 421 Pfam PF00883 Cytosol aminopeptidase family, catalytic domain
109 421 InterPro IPR000819 Peptidase M17, leucyl aminopeptidase, C-terminal
1 428 PIRSF PIRSF036388 Ctsl_amnpptdse_B
1 428 InterPro IPR008330 Peptidase M17, peptidase B
47 425 CDD cd00433 Peptidase_M17
47 425 InterPro IPR011356 Peptidase M17, leucine aminopeptidase/peptidase B
190 207 PRINTS PR00481 Cytosol aminopeptidase signature
190 207 InterPro IPR011356 Peptidase M17, leucine aminopeptidase/peptidase B
299 314 PRINTS PR00481 Cytosol aminopeptidase signature
299 314 InterPro IPR011356 Peptidase M17, leucine aminopeptidase/peptidase B
271 291 PRINTS PR00481 Cytosol aminopeptidase signature
271 291 InterPro IPR011356 Peptidase M17, leucine aminopeptidase/peptidase B
212 233 PRINTS PR00481 Cytosol aminopeptidase signature
212 233 InterPro IPR011356 Peptidase M17, leucine aminopeptidase/peptidase B
249 270 PRINTS PR00481 Cytosol aminopeptidase signature
249 270 InterPro IPR011356 Peptidase M17, leucine aminopeptidase/peptidase B
107 426 SUPERFAMILY SSF53187 Zn-dependent exopeptidases
98 427 FunFam G3DSA:3.40.630.10:FF:000037 Peptidase B

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
0.738
Likely same site as FPocket 5 2.0 Å 15 shared residues 83% of smaller site
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Surrounding area
Pocket 2 P2Rank #2
0.556
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Surrounding area
Pocket 3 P2Rank #3
0.245
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.082
Likely same site as FPocket 23 2.0 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 5 P2Rank #5
0.026
Likely same site as FPocket 5 6.1 Å 5 shared residues 71% 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 #23
0.566
Likely same site as P2Rank 4 2.0 Å 9 shared residues 100% of smaller site
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Surrounding area
Pocket 2 FPocket #5
0.365 Unusual size
Likely same site as P2Rank 1 2.0 Å 15 shared residues 83% of smaller site
Show in viewer
Surrounding area
Pocket 3 FPocket #18
0.29
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Surrounding area
Residue sets
UniProt: Active site:207-207
UniProt: Active site:281-281
UniProt: Binding site:195-195
UniProt: Binding site:200-200
UniProt: Binding site:218-218
UniProt: Binding site:277-277
UniProt: Binding site:279-279
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_A0A0H3H1H0
AlphaFold DB full sequence Viewing
ColabFold VK055_4646
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.

160 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 110 records from similar proteins
Structural ligands 10 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
1OT PDB via homolog 253.2 Da · LogP 1.01 · TPSA 101.4 Open detail RCSB PDB
3MW PDB via homolog Detail RCSB PDB
AHY PDB via homolog Detail RCSB PDB
BES PDB via homolog Detail RCSB PDB
DGZ 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
1OT RCSB PDB Q8IL11 253.2 Da LogP 1.01 TPSA 101.4 ✓ Ro5 ✓ Clean c1cnn(c1)c2ccc(cc2)[C@H](N)P(=O)(O)O
3MW RCSB PDB Q8IL11 351.4 Da LogP 1.43 TPSA 122.3 ✓ Ro5 ✓ Clean c1cnn(c1)c2ccc(cc2)[C@H](C(=O)NO)NC(=O)c3ccc(cc…
AHY RCSB PDB P00727 203.3 Da LogP 1.12 TPSA 83.5 ✓ Ro5 ✓ Clean CCCCCCC[C@H]([C@@H](C(=O)O)O)N
BES RCSB PDB O86436 308.4 Da LogP 0.53 TPSA 112.7 ✓ Ro5 ✓ Clean CC(C)C[C@@H](C(=O)O)NC(=O)[C@H]([C@@H](Cc1ccccc…
DGZ RCSB PDB Q8IL11 1010.2 Da LogP 2.97 TPSA 270.4 3 viol. ✓ Clean C#CCCCC(=O)NCCCCC(C(=O)N)NC(=O)C(Cc1ccc(cc1)C(=…
PLU RCSB PDB P00727 167.1 Da LogP 0.49 TPSA 83.6 ✓ Ro5 ✓ Clean CC(C)C[C@H](N)P(=O)(O)O
R5T RCSB PDB Q8IL11 332.4 Da LogP 1.94 TPSA 105.5 ✓ Ro5 ✓ Clean CC(C)(C)OC(=O)N[C@@H](c1ccc(cc1)n2cccn2)C(=O)NO
R5X RCSB PDB Q8IL11 351.4 Da LogP 1.43 TPSA 122.3 ✓ Ro5 ✓ Clean c1cc(cc(c1)N)C(=O)N[C@H](c2ccc(cc2)n3cccn3)C(=O…
TOD RCSB PDB Q8IL11 338.4 Da LogP 0.46 TPSA 136.0 ✓ Ro5 ✓ Clean CC(C)C[C@H]([C@@H](C(=O)NO)O)C(=O)N[C@@H](c1ccc…
ZED RCSB PDB P00727 325.5 Da LogP 2.40 TPSA 57.6 ✓ Ro5 ✓ Clean C[C@H](CS)C(=O)N1C[C@H](C[C@H]1C(=O)O)Sc2ccccc2

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 CHEMBL3359700 ChEMBL CHEMBL3359698 ChEMBL CHEMBL3359699 ChEMBL CHEMBL3359691 ChEMBL CHEMBL3359690 ChEMBL CHEMBL3359693 ChEMBL CHEMBL3359688 ChEMBL CHEMBL3359697 ChEMBL CHEMBL3359694 ChEMBL CHEMBL3359692 ChEMBL CHEMBL3359695 ChEMBL CHEMBL1090914 ChEMBL 2X0 ChEMBL CHEMBL2103847 ChEMBL CHEMBL289824 ChEMBL CHEMBL88808 ChEMBL CHEMBL327844 ChEMBL CHEMBL3355104 ChEMBL CHEMBL28650 ChEMBL CHEMBL4209822 ChEMBL CHEMBL3355106 ChEMBL 37B ChEMBL CHEMBL3355105 ChEMBL CHEMBL88476 ChEMBL CHEMBL2153736 ChEMBL CHEMBL328319 ChEMBL CHEMBL327182 ChEMBL CHEMBL3355110 ChEMBL CHEMBL284501 ChEMBL CHEMBL3359689 ChEMBL CHEMBL4206158 ChEMBL CHEMBL3355111 ChEMBL CHEMBL1689155 ChEMBL CHEMBL3355109 ChEMBL CHEMBL3355103 ChEMBL CHEMBL79092 ChEMBL CHEMBL3355108 ChEMBL CHEMBL1673064 ChEMBL CHEMBL3355100 ChEMBL CHEMBL3355101 ChEMBL 2WW ChEMBL CHEMBL1093530 ChEMBL CHEMBL89318 ChEMBL CHEMBL252204 ChEMBL CHEMBL78505 ChEMBL CHEMBL311875 ChEMBL CHEMBL68979 ChEMBL CHEMBL88179 ChEMBL CHEMBL1090913 ChEMBL CHEMBL1093247 ChEMBL PPH ChEMBL CHEMBL3359686 ChEMBL CHEMBL38475 ChEMBL CHEMBL134319 ChEMBL CHEMBL309130 ChEMBL CHEMBL305198 ChEMBL CHEMBL3355102 ChEMBL CHEMBL3143143 ChEMBL BEY ChEMBL CHEMBL1204264 ChEMBL CHEMBL40508 ChEMBL A4Z ChEMBL CHEMBL1299222 ChEMBL CHEMBL1326175 ChEMBL CHEMBL1342344 ChEMBL CHEMBL1361530 ChEMBL CHEMBL1367885 ChEMBL CHEMBL1370991 ChEMBL CHEMBL1374083 ChEMBL CHEMBL1384526 ChEMBL CHEMBL1392396 ChEMBL CHEMBL1400008 ChEMBL CHEMBL1412158 ChEMBL CHEMBL1421228 ChEMBL CHEMBL1422754 ChEMBL CHEMBL1424612 ChEMBL CHEMBL1433233 ChEMBL CHEMBL1438342 ChEMBL CHEMBL1444370 ChEMBL CHEMBL1462218 ChEMBL CHEMBL1463795 ChEMBL CHEMBL1464552 ChEMBL CHEMBL1481220 ChEMBL CHEMBL1490352 ChEMBL CHEMBL1490445 ChEMBL CHEMBL1492010 ChEMBL CHEMBL1492585 ChEMBL CHEMBL1499872 ChEMBL CHEMBL1506414 ChEMBL CHEMBL1510425 ChEMBL CHEMBL1517055 ChEMBL CHEMBL1535307 ChEMBL CHEMBL1538427 ChEMBL CHEMBL1538544 ChEMBL CHEMBL1558568 ChEMBL CHEMBL1568805 ChEMBL CHEMBL1572038 ChEMBL CHEMBL1587393 ChEMBL CHEMBL1596275 ChEMBL S16