Protein target profile

VK055_3786

peptide deformylase

Genome: KpATCC43816 Gene: def AIK82341.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3H3U3
Length 164
Pocket druggability 0.03
Metabolic reactions 1
Chokepoint No
Direct ligand evidence 0 162 total records
Functional annotation 0 EC 1 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 (%)
32.298 Lower values reduce human off-target concern.
Human E-value
3.64e-16
Gut microbiome similarity
5.8% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
93.293 Higher values support similarity to known essential genes.
DEG E-value
1.45e-110 Smaller values mean stronger essential-gene similarity.

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
97.06 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.03
Structure A0A0H3H3U3
Pocket Pocket 1
P2Rank 0.602
Structure A0A0H3H3U3
Pocket Pocket 1
ColabFold model
FPocket 0.259 · Pocket 1
P2Rank 0.679 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 277 / 4744 genomes with a hit
Prevalence 5.8%

Cross-references

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

Chemistry

ChEMBL CHEMBL365416 ChEMBL CHEMBL364836 ChEMBL CHEMBL441502 ChEMBL CHEMBL156257 ChEMBL CHEMBL156414 ChEMBL CHEMBL421252 ChEMBL CHEMBL156033 ChEMBL CHEMBL156163 ChEMBL CHEMBL158092 ChEMBL CHEMBL156187 ChEMBL CHEMBL156547 ChEMBL CHEMBL157738 ChEMBL CHEMBL160164 ChEMBL CHEMBL345440 ChEMBL CHEMBL346291 ChEMBL CHEMBL346581 ChEMBL CHEMBL347445 ChEMBL CHEMBL347977 ChEMBL CHEMBL348314 ChEMBL CHEMBL348888 ChEMBL CHEMBL154703 ChEMBL CHEMBL156201 ChEMBL CHEMBL156427 ChEMBL CHEMBL157091 ChEMBL CHEMBL157797 ChEMBL CHEMBL188671 ChEMBL CHEMBL409416 ChEMBL CHEMBL155998 ChEMBL CHEMBL156543 ChEMBL CHEMBL156546 ChEMBL CHEMBL160493 ChEMBL CHEMBL1643873 ChEMBL CHEMBL1796096 ChEMBL CHEMBL347204 ChEMBL CHEMBL1796098 ChEMBL CHEMBL330263 ChEMBL CHEMBL350211 ChEMBL CHEMBL160513 ChEMBL CHEMBL1796103 ChEMBL CHEMBL422175 ChEMBL CHEMBL84969 ChEMBL CHEMBL157712 ChEMBL CHEMBL1643872 ChEMBL CHEMBL1796230 ChEMBL CHEMBL346544 ChEMBL CHEMBL347418 ChEMBL CHEMBL157687 ChEMBL CHEMBL1796080 ChEMBL CHEMBL1796228 ChEMBL CHEMBL3706628 ChEMBL CHEMBL156080 ChEMBL CHEMBL1643875 ChEMBL CHEMBL1796097 ChEMBL CHEMBL1796101 ChEMBL CHEMBL1796104 ChEMBL CHEMBL1796105 ChEMBL CHEMBL1796225 ChEMBL CHEMBL1796226 ChEMBL CHEMBL329677 ChEMBL CHEMBL419878 ChEMBL CHEMBL91263 ChEMBL CHEMBL92954 ChEMBL CHEMBL94000 ChEMBL CHEMBL1208984 ChEMBL CHEMBL78128 ChEMBL CHEMBL361449 ChEMBL CHEMBL1208855 ChEMBL CHEMBL1208856 ChEMBL CHEMBL188894 ChEMBL CHEMBL1208854 ChEMBL CHEMBL1643874 ChEMBL CHEMBL1788203 ChEMBL CHEMBL1208985 ChEMBL CHEMBL1208983 ChEMBL CHEMBL1796089 ChEMBL CHEMBL1796102 ChEMBL CHEMBL1796106 ChEMBL CHEMBL1796229 ChEMBL CHEMBL328803 ChEMBL CHEMBL423047 ChEMBL CHEMBL88281 ChEMBL CHEMBL88547 ChEMBL CHEMBL88780 ChEMBL CHEMBL90012 ChEMBL CHEMBL90401 ChEMBL CHEMBL90925 ChEMBL CHEMBL91903 ChEMBL CHEMBL92844 ChEMBL CHEMBL93381 ChEMBL CHEMBL1209868 ChEMBL CHEMBL1643868 ChEMBL CHEMBL360609 ChEMBL CHEMBL78001 ChEMBL CHEMBL365910 ChEMBL CHEMBL386468 ChEMBL CHEMBL1209044 ChEMBL CHEMBL1643864 ChEMBL MDB ChEMBL CHEMBL1796227 ChEMBL CHEMBL90406

Metabolic context

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

Explore metabolic network
Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reaction

1 reaction mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MLHIPDERLRKVAEPVKEVNAEIQRIVDDMFDTMYAEEGIGLAATQVDIHQRIIVIDVSENREEQLVLINPEMLEKEGETGIEEGCLSIPEQRALVPRAEKVKIRALDRDGKPFELEADGLLAICIQHEMDHLVGKLFIDYLSPLKQQRIRQKVEKLDRLRSRA

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 GO

Gene Ontology (GO)

1
  • GO:0042586 Catalysis of the reaction: formyl-L-methionyl peptide + H2O = formate + methionyl peptide.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

25 records
Show feature table
Start End DB Term Name
2 159 PANTHER PTHR10458 PEPTIDE DEFORMYLASE
2 159 InterPro IPR023635 Peptide deformylase
1 155 NCBIfam TIGR00079 peptide deformylase
1 155 InterPro IPR023635 Peptide deformylase
1 163 FunFam G3DSA:3.90.45.10:FF:000001 Peptide deformylase
2 159 SUPERFAMILY SSF56420 Peptide deformylase
2 159 InterPro IPR036821 Peptide deformylase superfamily
96 114 PRINTS PR01576 Peptide deformylase signature
96 114 InterPro IPR023635 Peptide deformylase
28 57 PRINTS PR01576 Peptide deformylase signature
28 57 InterPro IPR023635 Peptide deformylase
84 95 PRINTS PR01576 Peptide deformylase signature
84 95 InterPro IPR023635 Peptide deformylase
115 144 PRINTS PR01576 Peptide deformylase signature
115 144 InterPro IPR023635 Peptide deformylase
1 163 PIRSF PIRSF004749 Pep_def
1 163 InterPro IPR023635 Peptide deformylase
1 164 Gene3D G3DSA:3.90.45.10 Peptide deformylase
1 164 InterPro IPR036821 Peptide deformylase superfamily
1 138 CDD cd00487 Pep_deformylase
1 138 InterPro IPR023635 Peptide deformylase
2 147 Pfam PF01327 Polypeptide deformylase
2 147 InterPro IPR023635 Peptide deformylase
1 157 Hamap MF_00163 Peptide deformylase [def].
1 157 InterPro IPR023635 Peptide deformylase

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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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

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.602
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.016
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:134-134
UniProt: Binding site:133-133
UniProt: Binding site:137-137
UniProt: Binding site:91-91
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_A0A0H3H3U3
AlphaFold DB full sequence Viewing
ColabFold VK055_3786
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.

162 records
Chemistry signal

Structural and bioactivity evidence are both available for this target.

Direct evidence 0 same-protein records
Transferred evidence 112 records from similar proteins
Structural ligands 12 0 loaded crystals
Measured bioactivity 100 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2BB PDB via homolog 345.4 Da · LogP 0.13 · TPSA 119.0 Open detail RCSB PDB
BB1 PDB via homolog Detail RCSB PDB
BB2 PDB via homolog Detail RCSB PDB
GNR PDB via homolog Detail RCSB PDB
H2S 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
2BB RCSB PDB P0A6K3 345.4 Da LogP 0.13 TPSA 119.0 ✓ Ro5 ✓ Clean CC(C)C[C@H]([C@@H](C(=O)NO)O)C(=O)N[C@H](C(=O)N…
BB1 RCSB PDB P0A6K3 329.4 Da LogP 1.26 TPSA 90.0 ✓ Ro5 ✓ Clean CCCC[C@H](CN(C=O)O)C(=O)N[C@H](C(=O)N(C)C)C(C)(…
BB2 RCSB PDB P0A6K3 385.5 Da LogP 1.20 TPSA 119.0 ✓ Ro5 ✓ Clean CCCCC[C@H](CC(=O)NO)C(=O)N[C@@H](C(C)C)C(=O)N1C…
GNR RCSB PDB Q9I7A8 238.3 Da LogP 0.99 TPSA 78.4 ✓ Ro5 ✓ Clean c1ccc2c(c1)NC(=O)[C@H](S2)CC(=O)NO
H2S RCSB PDB P0A6K3 34.1 Da LogP 0.11 TPSA 0.0 ✓ Ro5 ✓ Clean S
K1U RCSB PDB B0VNL8 342.4 Da LogP 3.46 TPSA 71.4 ✓ Ro5 ✓ Clean c1ccc(cc1)C[C@H](CC(=O)O)C(=O)SCC(=O)c2ccccc2
K2U RCSB PDB B0VNL8 316.4 Da LogP 3.57 TPSA 57.5 ✓ Ro5 ✓ Clean c1ccc(cc1)C[C@H](CC(=O)O)[C@H](O)SCc2ccccc2
K3U RCSB PDB B0VNL8 366.4 Da LogP 4.94 TPSA 34.1 ✓ Ro5 ✓ Clean c1ccc(cc1)C[C@H](CC(F)(F)F)C(=O)SCC(=O)c2ccccc2
LHY RCSB PDB B0VNL8 224.2 Da LogP 0.37 TPSA 98.7 ✓ Ro5 ✓ Clean c1ccc(cc1)C[C@@H](C(=O)O)NC(=O)NO
MHA RCSB PDB Q9I7A8 190.2 Da LogP -2.06 TPSA 120.9 ✓ Ro5 ✓ Clean C(C(=O)N)N(CC(=O)O)CC(=O)O
MLN RCSB PDB P0A6K3 445.4 Da LogP 2.73 TPSA 168.1 ✓ Ro5 ✓ Clean CCCC[C@@H](C(=O)N[C@@H](CC(C)C)C(=O)Nc1ccc(cc1)…
SB7 RCSB PDB P0A6K3 181.2 Da LogP 1.26 TPSA 43.7 ✓ Ro5 ✓ Clean c1ccc(cc1)CCCN(CO)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.