KpATCC43816 Protein target profile

pepP

Accession: VK055_4139

Gene: AIK82685.1 pepP 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GXD1

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Length 438

Pocket druggability (P2Rank · AlphaFold DB model) 0.73

Direct ligand evidence 0 55 total records

Functional annotation 1 EC 4 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.

Main supporting evidence

Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.73. Structure available AlphaFold DB model + ColabFold model Ligand evidence via structure/bioactivity 5 structural and 0 bioactivity records.

Risks to review

Evidence coverage

Core evidence streams are available for this target.

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 (%): 39.259 Lower values reduce human off-target concern.
Human E-value: 9.95e-24
Gut microbiome similarity: 2.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG): Y
DEG identity (%): 54.167 Higher values support similarity to known essential genes.
DEG E-value: 7.95e-172 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT: 98.39 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) 0.73

Structure A0A0H3GXD1

Pocket Pocket 1

Druggability (FPocket) 0.191

Structure A0A0H3GXD1

Pocket Pocket 3

ColabFold model

P2Rank 0.687 · Pocket 1

FPocket 0.243 · Pocket 2

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 133 / 4744 genomes with a hit

Prevalence 2.8%

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.

MTQQEFLSRRQTLLAQMQPGSAALIFAAPEAVRSADSEYPYRQNSDFWYFTGFNEPEALLVLIKSDETHNHSVLFNRVRDLTAEIWFGRRLGQEAAPAKLGVDRALAFSEINQQLYQLLNGLDAIYFAQGEYAYADEIVFNALEKLRKGSRQNLQAPNSVIDWRPIVHEMRLFKSAEELAVMRRAGEITALAHTRAMEKCRPGMFEYQLEGEILHEFNRHGARFPSYNTIVGGGENGCILHYTENESELRDGDLVLIDAGCEYRGYAGDITRTFPVNGKFTQPQREIYDIVLESLETALKLYRPGTSICQVNQEVVRIMITGLVRLGILKGEIDELIANNAHRPYFMHGLSHWLGLDVHDVGNYDTDRSRVLEPGMVLTVEPGLYIATDADVPAQYRGIGIRIEDDIVITEDGNENLTAGVVKKADEIEALMAAARQS

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Subcellular localization

Localization: Cytoplasmic

Enzyme Commission (EC)

3.4.11.9

Gene Ontology (GO)

GO:0030145 Binding to a manganese ion (Mn).
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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0006508 The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

23 records

Show feature table

Start	End	DB	Term	Name
173	438	Gene3D	G3DSA:3.90.230.10	Creatinase/methionine aminopeptidase superfamily
173	438	InterPro	IPR036005	Creatinase/aminopeptidase-like
1	136	SMART	SM01011	AMP_N_2
1	136	InterPro	IPR007865	Aminopeptidase P, N-terminal
182	411	Pfam	PF00557	Metallopeptidase family M24
182	411	InterPro	IPR000994	Peptidase M24
348	360	ProSitePatterns	PS00491	Aminopeptidase P and proline dipeptidase signature.
348	360	InterPro	IPR001131	Peptidase M24B, X-Pro dipeptidase/aminopeptidase P, conserved site
253	269	PRINTS	PR00599	Methionine aminopeptidase-1 signature
253	269	InterPro	IPR001714	Peptidase M24, methionine aminopeptidase
370	382	PRINTS	PR00599	Methionine aminopeptidase-1 signature
370	382	InterPro	IPR001714	Peptidase M24, methionine aminopeptidase
173	438	FunFam	G3DSA:3.90.230.10:FF:000002	Xaa-Pro aminopeptidase 3
2	174	SUPERFAMILY	SSF53092	Creatinase/prolidase N-terminal domain
2	174	InterPro	IPR029149	Creatinase/Aminopeptidase P/Spt16, N-terminal
1	171	Gene3D	G3DSA:3.40.350.10	-
1	171	InterPro	IPR029149	Creatinase/Aminopeptidase P/Spt16, N-terminal
2	434	PANTHER	PTHR43226	XAA-PRO AMINOPEPTIDASE 3
175	433	SUPERFAMILY	SSF55920	Creatinase/aminopeptidase
175	433	InterPro	IPR036005	Creatinase/aminopeptidase-like
179	419	CDD	cd01087	Prolidase
8	126	Pfam	PF05195	Aminopeptidase P, N-terminal domain
8	126	InterPro	IPR007865	Aminopeptidase P, 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

0.73

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Surrounding area

Pocket 2 P2Rank #2

0.159

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Surrounding area

Pocket 3 P2Rank #3

0.05

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Surrounding area

Pocket 4 P2Rank #4

0.039

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Surrounding area

Pocket 5 P2Rank #5

0.031

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Surrounding area

Binding pockets · P2Rank

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

Pocket 1 P2Rank #1

0.687

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Surrounding area

Pocket 2 P2Rank #2

0.116

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Surrounding area

Pocket 3 P2Rank #3

0.086

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Surrounding area

Pocket 4 P2Rank #4

0.048

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Surrounding area

Pocket 5 P2Rank #5

0.022

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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_A0A0H3GXD1	AlphaFold DB	—	—	full sequence	—	Viewing
ColabFold VK055_4139	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.

55 records

Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records

Transferred evidence 5 records from similar proteins

Structural ligands 5 0 loaded crystals

Measured bioactivity 0 direct and transferred ChEMBL records

Proposed compounds 50 similarity-based ZINC candidates

Best available ligand signal

01B PDB via homolog 195.2 Da · LogP 0.00 · TPSA 83.5 Open detail RCSB PDB

12P PDB via homolog Detail RCSB PDB

FLC PDB via homolog Detail RCSB PDB

JEF PDB via homolog Detail RCSB PDB

XPE PDB via homolog Detail RCSB PDB

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

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.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
01B RCSB PDB	5X49	Q9NQH7	195.2 Da LogP 0.00 TPSA 83.5	✓ Ro5	✓ Clean	`c1ccc(cc1)C[C@H]([C@@H](C(=O)O)O)N`
12P RCSB PDB	5X49	Q9NQH7	546.7 Da LogP -0.85 TPSA 142.0	2 viol.	✓ Clean	`C(COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO)O`
FLC RCSB PDB	2BHA	P15034	189.1 Da LogP -5.25 TPSA 140.6	✓ Ro5	✓ Clean	`C(C(=O)[O-])C(CC(=O)[O-])(C(=O)[O-])O`
JEF RCSB PDB	6A9T	P40051	597.8 Da LogP 3.24 TPSA 118.3	2 viol.	✓ Clean	`C[C@@H](COC[C@@H](C)OC[C@@H](C)OC[C@H](C)OC[C@H…`
XPE RCSB PDB	1WL6	P15034	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`C(COCCOCCOCCOCCOCCOCCOCCOCCOCCO)O`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

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

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC12501520 ZINC	1.000	458.5 Da LogP -0.88 TPSA 123.5	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC3874716 ZINC	1.000	414.5 Da LogP -0.90 TPSA 114.3	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC4283769 ZINC	1.000	238.3 Da LogP -0.96 TPSA 77.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCO`
ZINC4521548 ZINC	1.000	282.3 Da LogP -0.95 TPSA 86.6	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCO`
ZINC5178829 ZINC	1.000	326.4 Da LogP -0.93 TPSA 95.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCO`
ZINC5178830 ZINC	1.000	370.4 Da LogP -0.91 TPSA 105.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC115086873 ZINC	0.688	209.2 Da LogP -1.08 TPSA 83.2	✓ Ro5	✓ Clean	`NOCCOCCOCCOCCO`
ZINC13354127 ZINC	0.688	209.2 Da LogP 0.09 TPSA 72.5	✓ Ro5	✓ Clean	`COC(=O)[C@H](O)[C@@H](N)Cc1ccccc1`
ZINC13354130 ZINC	0.688	209.2 Da LogP 0.09 TPSA 72.5	✓ Ro5	✓ Clean	`COC(=O)[C@@H](O)[C@@H](N)Cc1ccccc1`
ZINC137432264 ZINC	0.688	457.6 Da LogP -0.91 TPSA 129.3	1 viol.	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC146143823 ZINC	0.688	237.3 Da LogP -1.00 TPSA 83.2	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCO`
ZINC1542984442 ZINC	0.688	413.5 Da LogP -0.93 TPSA 120.1	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1565503710 ZINC	0.688	254.3 Da LogP -0.03 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCS`
ZINC1580161 ZINC	0.688	208.3 Da LogP -0.33 TPSA 57.2	✓ Ro5	✓ Clean	`COCCOCCOCCOCCO`
ZINC16052118 ZINC	0.688	340.4 Da LogP -0.28 TPSA 84.8	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCO`
ZINC16052257 ZINC	0.688	384.5 Da LogP -0.26 TPSA 94.1	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC1857792028 ZINC	0.688	430.6 Da LogP 0.04 TPSA 94.1	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC1857792057 ZINC	0.688	474.6 Da LogP 0.06 TPSA 103.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC230494776 ZINC	0.688	325.4 Da LogP -0.96 TPSA 101.6	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCO`
ZINC34317654 ZINC	0.688	472.6 Da LogP -0.23 TPSA 112.5	1 viol.	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC38917157 ZINC	0.688	210.3 Da LogP -0.04 TPSA 47.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCS`
ZINC44076059 ZINC	0.688	428.5 Da LogP -0.24 TPSA 103.3	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC5210101 ZINC	0.688	252.3 Da LogP -0.31 TPSA 66.4	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCO`
ZINC5650743 ZINC	0.688	222.3 Da LogP 0.07 TPSA 57.2	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCO`
ZINC5997860 ZINC	0.688	296.4 Da LogP -0.29 TPSA 75.6	✓ Ro5	✓ Clean	`COCCOCCOCCOCCOCCOCCO`
ZINC6403917 ZINC	0.688	354.4 Da LogP 0.11 TPSA 84.8	✓ Ro5	✓ Clean	`CCOCCOCCOCCOCCOCCOCCOCCO`
ZINC77271182 ZINC	0.688	281.3 Da LogP -0.98 TPSA 92.4	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCO`
ZINC83253921 ZINC	0.688	369.5 Da LogP -0.95 TPSA 110.9	✓ Ro5	✓ Clean	`NCCOCCOCCOCCOCCOCCOCCOCCO`
ZINC90741446 ZINC	0.688	386.5 Da LogP 0.02 TPSA 84.8	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCOCCOCCS`
ZINC90741447 ZINC	0.688	298.4 Da LogP -0.01 TPSA 66.4	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCCOCCS`
ZINC140096846 ZINC	0.677	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](CCc1ccccc1)[C@@H](O)C(=O)O`
ZINC140096989 ZINC	0.677	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](CCc1ccccc1)[C@H](O)C(=O)O`
ZINC38867114 ZINC	0.677	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](CCc1ccccc1)[C@H](O)C(=O)O`
ZINC38867116 ZINC	0.677	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](CCc1ccccc1)[C@@H](O)C(=O)O`
ZINC60123716 ZINC	0.667	223.3 Da LogP 0.48 TPSA 72.5	✓ Ro5	✓ Clean	`CCOC(=O)[C@@H](O)[C@@H](N)Cc1ccccc1`
ZINC144169243 ZINC	0.647	281.3 Da LogP -1.37 TPSA 89.4	✓ Ro5	✓ Clean	`OCCOCCOCCNCCOCCOCCO`
ZINC205758716 ZINC	0.647	457.6 Da LogP -1.31 TPSA 126.3	1 viol.	✓ Clean	`OCCOCCOCCOCCOCCNCCOCCOCCOCCOCCO`
ZINC2569682 ZINC	0.647	251.3 Da LogP 1.26 TPSA 72.5	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@H](O)[C@@H](N)Cc1ccccc1`
ZINC2569683 ZINC	0.647	251.3 Da LogP 1.26 TPSA 72.5	✓ Ro5	✓ Clean	`CC(C)(C)OC(=O)[C@@H](O)[C@H](N)Cc1ccccc1`
ZINC575441396 ZINC	0.647	369.5 Da LogP -1.34 TPSA 107.9	✓ Ro5	✓ Clean	`OCCOCCOCCOCCNCCOCCOCCOCCO`
ZINC2526314 ZINC	0.625	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)[C@@H](O)CC(=O)O`
ZINC2598915 ZINC	0.625	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1)[C@@H](O)CC(=O)O`
ZINC2598917 ZINC	0.625	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)[C@H](O)CC(=O)O`
ZINC2598919 ZINC	0.625	209.2 Da LogP 0.39 TPSA 83.5	✓ Ro5	✓ Clean	`N[C@H](Cc1ccccc1)[C@H](O)CC(=O)O`
ZINC34514743 ZINC	0.615	240.3 Da LogP 2.13 TPSA 52.0	✓ Ro5	✓ Clean	`N[C@@H](Cc1ccccc1)[C@@H](N)Cc1ccccc1`
ZINC1644613 ZINC	0.611	206.3 Da LogP 0.83 TPSA 47.9	✓ Ro5	✓ Clean	`CCCCOCCOCCOCCO`
ZINC258839852 ZINC	0.611	276.3 Da LogP 0.61 TPSA 57.2	✓ Ro5	✓ Clean	`OCCOCCOCCOCCOCC(F)(F)F`
ZINC167715346 ZINC	0.600	266.3 Da LogP -0.18 TPSA 77.4	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCOCCCO`
ZINC34160867 ZINC	0.600	222.3 Da LogP -0.20 TPSA 68.2	✓ Ro5	✓ Clean	`OCCCOCCOCCOCCCO`
ZINC1569729 ZINC	0.593	202.3 Da LogP -0.05 TPSA 92.4	✓ Ro5	✓ Clean	`CC(C)C[C@H](N)C(=O)N[C@H](C)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.

Sequence

UniProt A0A0H3GXD1

pepP

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

Main supporting evidence

Risks to review

Evidence coverage

Prioritization evidence

Off-target risk

Essentiality

Structure confidence

Binding-site evidence

Metabolic context

Sequence

Functional annotations

Subcellular localization

Enzyme Commission (EC)

Gene Ontology (GO)

Sequence domains and features

3D structure

Binding pockets · P2Rank

Binding pockets · P2Rank

Binding pockets · FPocket

Structural evidence

Ligand evidence

Cross-references

Sequence